<86>Apr 21 04:07:54 userdel[18161]: delete user 'rooter' <86>Apr 21 04:07:54 userdel[18161]: removed group 'rooter' owned by 'rooter' <86>Apr 21 04:07:54 userdel[18161]: removed shadow group 'rooter' owned by 'rooter' <86>Apr 21 04:07:54 groupadd[18176]: group added to /etc/group: name=rooter, GID=561 <86>Apr 21 04:07:54 groupadd[18176]: group added to /etc/gshadow: name=rooter <86>Apr 21 04:07:54 groupadd[18176]: new group: name=rooter, GID=561 <86>Apr 21 04:07:54 useradd[18186]: new user: name=rooter, UID=561, GID=561, home=/root, shell=/bin/bash <86>Apr 21 04:07:54 userdel[18204]: delete user 'builder' <86>Apr 21 04:07:54 userdel[18204]: removed group 'builder' owned by 'builder' <86>Apr 21 04:07:54 userdel[18204]: removed shadow group 'builder' owned by 'builder' <86>Apr 21 04:07:54 groupadd[18225]: group added to /etc/group: name=builder, GID=562 <86>Apr 21 04:07:54 groupadd[18225]: group added to /etc/gshadow: name=builder <86>Apr 21 04:07:54 groupadd[18225]: new group: name=builder, GID=562 <86>Apr 21 04:07:54 useradd[18235]: new user: name=builder, UID=562, GID=562, home=/usr/src, shell=/bin/bash <13>Apr 21 04:08:01 rpmi: tex-common-0.2-alt4 1244804096 installed <13>Apr 21 04:08:01 rpmi: texlive-common-0.1-alt3 1244804816 installed <13>Apr 21 04:08:01 rpmi: perl-Encode-2.83-alt1 1459157776 installed <13>Apr 21 04:08:01 rpmi: libjpeg-2:1.3.1-alt0.1 1388074033 installed <13>Apr 21 04:08:01 rpmi: xorg-xproto-devel-7.0.31-alt0.M80P.1 p8+226471.100.1.1 1554301566 installed <13>Apr 21 04:08:01 rpmi: libpng15-1.5.28-alt1 1484572014 installed <13>Apr 21 04:08:01 rpmi: ca-certificates-2016.02.25-alt1 1462368370 installed <13>Apr 21 04:08:01 rpmi: libcrypto10-1.0.2n-alt0.M80P.1 1512766129 installed <13>Apr 21 04:08:01 rpmi: libexpat-2.2.4-alt0.M80P.1 1503871120 installed <13>Apr 21 04:08:01 rpmi: libtiff5-4.0.3-alt1 1348347498 installed <13>Apr 21 04:08:01 rpmi: liblcms2-2.8-alt1 1471601528 installed <13>Apr 21 04:08:01 rpmi: perl-HTTP-Date-6.02-alt1 1348645274 installed <13>Apr 21 04:08:01 rpmi: libopenblas-0.2.14-alt1.git20150324 1433158855 installed <13>Apr 21 04:08:01 rpmi: libwayland-client-1.14.0-alt0.M80P.1 1502720500 installed <13>Apr 21 04:08:01 rpmi: libpng12-1.2.50-alt2 1347753407 installed <13>Apr 21 04:08:01 rpmi: perl-XML-NamespaceSupport-1.11-alt3 1322003535 installed <13>Apr 21 04:08:01 rpmi: libsqlite3-3.15.2-alt1 1480432212 installed <13>Apr 21 04:08:02 rpmi: libnspr-1:4.20-alt1 p8.216526.40 1542382588 installed <13>Apr 21 04:08:02 rpmi: libnss-3.40.0-alt0.M80P.1 p8.216526.44 1542814585 installed <13>Apr 21 04:08:02 rpmi: libtasn1-4.9-alt1 1469555628 installed <13>Apr 21 04:08:02 rpmi: libidn2-2.0.4-alt3.M80P.1 1520307194 installed <13>Apr 21 04:08:02 rpmi: libkpathsea-2008.0-alt0.15.6 1449446882 installed <13>Apr 21 04:08:02 rpmi: libICE-1.0.9-alt1 1409902719 installed <13>Apr 21 04:08:02 rpmi: libgdbm-1.8.3-alt10 1454943313 installed <13>Apr 21 04:08:02 rpmi: libSM-1.2.2-alt1 1391072686 installed <13>Apr 21 04:08:02 rpmi: libjasper-1.900.1-alt3 1391718482 installed <13>Apr 21 04:08:02 rpmi: perl-Term-ANSIColor-4.05-alt1 1458575791 installed <13>Apr 21 04:08:02 rpmi: rpm-macros-info-install-6.0-alt3 1449879498 installed <13>Apr 21 04:08:02 rpmi: libtcl-8.5.9-alt2 1351878901 installed <13>Apr 21 04:08:02 rpmi: tcl-8.5.9-alt2 1351878901 installed <13>Apr 21 04:08:02 rpmi: zlib-devel-1.2.8-alt1 1371079009 installed <13>Apr 21 04:08:02 rpmi: libwayland-server-1.14.0-alt0.M80P.1 1502720500 installed <13>Apr 21 04:08:02 rpmi: perl-LWP-MediaTypes-6.02-alt1 1329754558 installed <13>Apr 21 04:08:02 rpmi: perl-Compress-Raw-Zlib-2.069-alt1.1 1448470036 installed <13>Apr 21 04:08:02 rpmi: perl-libnet-1:3.08-alt1 1458419902 installed <13>Apr 21 04:08:02 rpmi: perl-URI-1.71-alt1 1455181348 installed <13>Apr 21 04:08:02 rpmi: perl-XML-SAX-Base-1.08-alt1 1317871344 installed <13>Apr 21 04:08:02 rpmi: libnettle6-3.4.1-alt1 p8.217493.100 1544204548 installed <13>Apr 21 04:08:02 rpmi: libopenjpeg2.0-2.2.0-alt0.M80P.1 1503526491 installed <13>Apr 21 04:08:02 rpmi: libquadmath0-5.3.1-alt3.M80P.1 p8+225520.100.3.1 1553688800 installed <13>Apr 21 04:08:02 rpmi: libgfortran3-5.3.1-alt3.M80P.1 p8+225520.100.3.1 1553688800 installed <13>Apr 21 04:08:02 rpmi: t1lib-5.1.2-alt5 1326979643 installed <13>Apr 21 04:08:02 rpmi: libXau-1.0.8-alt1 1369565807 installed <13>Apr 21 04:08:02 rpmi: libXau-devel-1.0.8-alt1 1369565807 installed <13>Apr 21 04:08:02 rpmi: libquadmath5-devel-5.3.1-alt3.M80P.1 p8+225520.100.3.1 1553688800 installed <13>Apr 21 04:08:02 rpmi: libhogweed4-3.4.1-alt1 p8.217493.100 1544204548 installed <13>Apr 21 04:08:02 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed <13>Apr 21 04:08:02 rpmi: libpng-devel-1.5.28-alt1 1484572014 installed <13>Apr 21 04:08:02 rpmi: perl-DBM-1:5.22.3-alt0.M80P.1 1485958065 installed <13>Apr 21 04:08:02 rpmi: libICE-devel-1.0.9-alt1 1409902719 installed <13>Apr 21 04:08:02 rpmi: libSM-devel-1.2.2-alt1 1391072686 installed <13>Apr 21 04:08:02 rpmi: nss-utils-3.40.0-alt0.M80P.1 p8.216526.44 1542814585 installed <13>Apr 21 04:08:02 rpmi: libwayland-cursor-1.14.0-alt0.M80P.1 1502720500 installed <13>Apr 21 04:08:02 rpmi: libopenblas-devel-0.2.14-alt1.git20150324 1433158855 installed <13>Apr 21 04:08:02 rpmi: perl-File-Listing-6.04-alt1 1329758996 installed <13>Apr 21 04:08:02 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed <13>Apr 21 04:08:02 rpmi: perl-IO-HTML-1.001-alt1 1404821752 installed <13>Apr 21 04:08:02 rpmi: perl-libintl-1.24-alt1.1 1448485129 installed <13>Apr 21 04:08:02 rpmi: fonts-type1-tipa-tex-1.3-alt4 1246545601 installed <13>Apr 21 04:08:02 rpmi: texlive-doc-base-2008.0-alt0.10 1238420746 installed <13>Apr 21 04:08:03 rpmi: texmf-tex4ht-1.0.2009_06_11_1038-alt1 1328304130 installed <13>Apr 21 04:08:03 rpmi: java-stub-javadoc-0.1-alt1 1229813340 installed <13>Apr 21 04:08:03 rpmi: tcsh-6.18.01-alt2 1442313244 installed <13>Apr 21 04:08:03 rpmi: rpm-build-tcl-0.4-alt2 1445508295 installed <13>Apr 21 04:08:03 rpmi: tcl-devel-8.5.9-alt2 1351878901 installed <13>Apr 21 04:08:03 rpmi: rpm-macros-java-1:4.6.0-alt9_12jpp8.1.1 1460387057 installed <13>Apr 21 04:08:03 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed <13>Apr 21 04:08:03 rpmi: perl-Unicode-EastAsianWidth-1.33-alt1 1383358357 installed <13>Apr 21 04:08:03 rpmi: perl-Text-Unidecode-1.27-alt1 1445859908 installed <13>Apr 21 04:08:03 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed <13>Apr 21 04:08:03 rpmi: perl-Pod-Simple-3.32-alt1 1447205413 installed <13>Apr 21 04:08:03 rpmi: libtre5-0.8.0-alt2.1 1334590818 installed <13>Apr 21 04:08:03 rpmi: libruby-2.5.1-alt0.M80P.1 1525659669 installed <13>Apr 21 04:08:03 rpmi: ruby-2.5.1-alt0.M80P.1 1525659669 installed <13>Apr 21 04:08:03 rpmi: poppler-data-0.4.8-alt1.M80P.1 1524561858 installed <13>Apr 21 04:08:03 rpmi: libpcre16-8.40-alt1 1484570205 installed <13>Apr 21 04:08:03 rpmi: pcretest-8.40-alt1 1484570205 installed <13>Apr 21 04:08:03 rpmi: libnumpy-py3-1:1.12.1-alt0.M80P.1 1496160663 installed <13>Apr 21 04:08:03 rpmi: libxblas-1.0.248-alt1 1322010716 installed <13>Apr 21 04:08:03 rpmi: liblapack-1:3.5.0-alt1 1401382194 installed <13>Apr 21 04:08:03 rpmi: libxkbcommon-0.7.2-alt0.M80P.1 1503524837 installed <13>Apr 21 04:08:03 rpmi: libgudev-1:231-alt0.M80P.1 1487052830 installed <13>Apr 21 04:08:03 rpmi: udev-rules-1:239-alt1.M80P.1 p8+226956.200.2.1 1555431539 installed <13>Apr 21 04:08:03 rpmi: libepoxy-1.4.3-alt0.M80P.1 1498727071 installed <13>Apr 21 04:08:03 rpmi: libdatrie-0.2.8-alt1_5 1410185969 installed <13>Apr 21 04:08:03 rpmi: libthai-0.1.24-alt1_1 1459282110 installed <13>Apr 21 04:08:03 rpmi: publicsuffix-list-dafsa-20190329-alt1 p8+226349.100.1.1 1554128046 installed <13>Apr 21 04:08:03 rpmi: libpsl-0.18.0-alt0.M80P.1 1502785107 installed <13>Apr 21 04:08:03 rpmi: libnghttp2-1.8.0-alt1 1456818805 installed <13>Apr 21 04:08:03 rpmi: libusb-1.0.21-alt0.M80P.1 1485147102 installed <13>Apr 21 04:08:03 rpmi: libpixman-3:0.32.8-alt1 1447610691 installed <13>Apr 21 04:08:03 rpmi: libbrotlicommon0-1.0.4-alt0.M80P.1 1528205024 installed <13>Apr 21 04:08:03 rpmi: libbrotlidec0-1.0.4-alt0.M80P.1 1528205024 installed <13>Apr 21 04:08:03 rpmi: xorg-renderproto-devel-0.11.1-alt3 1303465056 installed <13>Apr 21 04:08:03 rpmi: xorg-xextproto-devel-2:7.3.0-alt1 1389258977 installed <13>Apr 21 04:08:03 rpmi: xorg-kbproto-devel-1.0.6-alt1 1332531883 installed <13>Apr 21 04:08:03 rpmi: libxshmfence-1.2-alt1 1420972191 installed <13>Apr 21 04:08:03 rpmi: libpciaccess-1:0.13.4-alt1 1431681688 installed <13>Apr 21 04:08:03 rpmi: libdrm-1:2.4.89-alt1.M80P.1 1516609380 installed <13>Apr 21 04:08:03 rpmi: libgbm-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 21 04:08:03 rpmi: mailx-8.1.2-alt7 1366314831 installed <13>Apr 21 04:08:04 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed <13>Apr 21 04:08:04 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed <13>Apr 21 04:08:04 rpmi: libjbig-2.1-alt1 1401380921 installed <13>Apr 21 04:08:04 rpmi: xorg-rgb-1.0.4-alt1.qa1 1366268675 installed <13>Apr 21 04:08:04 rpmi: libnetpbm-10.35.97-alt1 1447854203 installed <13>Apr 21 04:08:04 rpmi: netpbm-10.35.97-alt1 1447854203 installed <13>Apr 21 04:08:04 rpmi: libgif-4.1.6-alt3 1299634266 installed <13>Apr 21 04:08:04 rpmi: libalsa-1:1.1.0-alt1.1.1 1454429213 installed <13>Apr 21 04:08:04 rpmi: liblua5.3-5.3.4-alt1.M80P.1 1533735694 installed <13>Apr 21 04:08:04 rpmi: lua5.3-5.3.4-alt1.M80P.1 1533735694 installed <13>Apr 21 04:08:04 rpmi: javapackages-tools-1:4.6.0-alt9_12jpp8.1.1 1460387057 installed <13>Apr 21 04:08:04 rpmi: java-common-1.5.0-alt1 1329330500 installed <13>Apr 21 04:08:04 rpmi: liblksctp-1.0.16-alt1 1392950081 installed <13>Apr 21 04:08:04 rpmi: lksctp-tools-1.0.16-alt1 1392950081 installed <13>Apr 21 04:08:04 rpmi: tzdata-java-2018g-alt0.M80P.1 p8.215998.100 1541069800 installed <13>Apr 21 04:08:05 rpmi: libicu56-1:5.6.1-alt1.1 1458012333 installed <13>Apr 21 04:08:05 rpmi: icu-utils-1:5.6.1-alt1.1 1458012333 installed <13>Apr 21 04:08:05 rpmi: perl-IO-Socket-IP-0.37-alt1 1444921335 installed <13>Apr 21 04:08:05 rpmi: perl-Compress-Raw-Bzip2-2.069-alt1.1 1448470068 installed <13>Apr 21 04:08:05 rpmi: perl-IO-Compress-2.069-alt1 1444618007 installed <13>Apr 21 04:08:05 rpmi: perl-HTTP-Message-6.11-alt1 1444616672 installed <13>Apr 21 04:08:05 rpmi: perl-HTTP-Cookies-6.01-alt1 1329759964 installed <13>Apr 21 04:08:05 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed <13>Apr 21 04:08:05 rpmi: perl-Net-HTTP-6.09-alt1 1432310023 installed <13>Apr 21 04:08:05 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed <13>Apr 21 04:08:05 rpmi: perl-HTML-Parser-3.72-alt1 1455170565 installed <13>Apr 21 04:08:05 rpmi: perl-libwww-6.15-alt1 1449505512 installed <13>Apr 21 04:08:05 rpmi: libgdk-pixbuf-locales-2.36.11-alt0.M80P.1 1507198237 installed <13>Apr 21 04:08:05 rpmi: gtk+3-themes-incompatible-3.20-alt3 1461944560 installed <13>Apr 21 04:08:05 rpmi: xml-utils-1:2.9.4.0.12.e905-alt1 1488560683 installed <13>Apr 21 04:08:05 rpmi: rpm-build-gir-0.7.2-alt3 1489330162 installed <13>Apr 21 04:08:05 rpmi: libproxy-0.4.14-alt0.M80P.1 1491211278 installed <13>Apr 21 04:08:05 rpmi: libpaper-1.1.24-alt4 1315383473 installed <13>Apr 21 04:08:05 rpmi: gcc-fortran-common-1.4.20-alt1 1432315196 installed <13>Apr 21 04:08:05 rpmi: libgfortran5-devel-5.3.1-alt3.M80P.1 p8+225520.100.3.1 1553688800 installed <13>Apr 21 04:08:05 rpmi: gcc-c++-common-1.4.20-alt1 1432315196 installed <13>Apr 21 04:08:05 rpmi: libstdc++5-devel-5.3.1-alt3.M80P.1 p8+225520.100.3.1 1553688800 installed <13>Apr 21 04:08:05 rpmi: libgraphite2-1.3.10-alt0.M80P.1 1496411360 installed <13>Apr 21 04:08:05 rpmi: ca-certificates-java-0.01-alt1 1316102488 installed <13>Apr 21 04:08:05 rpmi: bc-1:1.06-alt4 1461014962 installed <13>Apr 21 04:08:05 rpmi: libatk-locales-2.24.0-alt0.M80P.1 1504535386 installed <13>Apr 21 04:08:05 rpmi: libatk-2.24.0-alt0.M80P.1 1504535253 installed <13>Apr 21 04:08:05 rpmi: rpm-build-xdg-0.2-alt1 1250461503 installed <13>Apr 21 04:08:05 rpmi: shared-mime-info-1.9-alt0.M80P.1 1506021412 installed <13>Apr 21 04:08:05 rpmi: gsettings-desktop-schemas-data-3.24.1-alt0.M80P.1 1504768054 installed <13>Apr 21 04:08:05 rpmi: liblz4-1:1.7.5-alt1 1488766699 installed <13>Apr 21 04:08:05 rpmi: libgpg-error-1.31-alt1.M80P.1 1529024730 installed <13>Apr 21 04:08:05 rpmi: libgcrypt20-1.8.3-alt4 p8+219793.200.6.1 1551112986 installed <13>Apr 21 04:08:05 rpmi: libsystemd-1:239-alt1.M80P.1 p8+226956.200.2.1 1555431492 installed <13>Apr 21 04:08:05 rpmi: libdbus-1.10.24-alt4.M80P.1 1518773282 installed <13>Apr 21 04:08:06 rpmi: libavahi-0.6.31-alt7.M80P.1 1526318593 installed <13>Apr 21 04:08:06 rpmi: libxslt-1.1.28-alt4 1448210404 installed <13>Apr 21 04:08:06 rpmi: libX11-locales-3:1.6.3-alt1 1431956885 installed <13>Apr 21 04:08:06 rpmi: libXdmcp-1.1.1-alt1 1334617699 installed <13>Apr 21 04:08:06 rpmi: libxcb-1.12-alt2 p8.218219.300 1545313310 installed <13>Apr 21 04:08:06 rpmi: libX11-3:1.6.3-alt1 1431956911 installed <13>Apr 21 04:08:06 rpmi: libXext-1.3.3-alt1 1409902932 installed <13>Apr 21 04:08:06 rpmi: libXrender-0.9.8-alt1 1371312110 installed <13>Apr 21 04:08:06 rpmi: libXt-1.1.4-alt1 1369984716 installed <13>Apr 21 04:08:06 rpmi: libXpm-3.5.11-alt1 1391072398 installed <13>Apr 21 04:08:06 rpmi: libXmu-1.1.2-alt1 1391072528 installed <13>Apr 21 04:08:06 rpmi: libXfixes-5.0.1-alt1 1369809606 installed <13>Apr 21 04:08:06 rpmi: libXtst-1.2.2-alt1 1369984880 installed <13>Apr 21 04:08:06 rpmi: libXi-1.7.9-alt1.M80P.1 1515766146 installed <13>Apr 21 04:08:06 rpmi: libat-spi2-core-2.24.1-alt0.M80P.1 1504536015 installed <13>Apr 21 04:08:06 rpmi: libXdamage-1.1.3-alt4 1297162596 installed <13>Apr 21 04:08:07 rpmi: libxcb-devel-1.12-alt2 p8.218219.300 1545313310 installed <13>Apr 21 04:08:07 rpmi: libX11-devel-3:1.6.3-alt1 1431956911 installed <13>Apr 21 04:08:07 rpmi: libXrender-devel-0.9.8-alt1 1371312110 installed <13>Apr 21 04:08:07 rpmi: libXext-devel-1.3.3-alt1 1409902932 installed <13>Apr 21 04:08:07 rpmi: libXt-devel-1.1.4-alt1 1369984716 installed <13>Apr 21 04:08:07 rpmi: libXcursor-1.1.15-alt1.M80P.1 1512373713 installed <13>Apr 21 04:08:07 rpmi: libXaw-1.0.12-alt1 1391072621 installed <13>Apr 21 04:08:07 rpmi: libXrandr-1.5.0-alt1 1431936188 installed <13>Apr 21 04:08:07 rpmi: libXxf86vm-1.1.3-alt1 1369984824 installed <13>Apr 21 04:08:07 rpmi: libGL-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 21 04:08:07 rpmi: libEGL-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 21 04:08:07 rpmi: libEGL-devel-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 21 04:08:07 rpmi: libGL-devel-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 21 04:08:07 rpmi: libwayland-egl-4:18.0.5-alt1.M80P.1 p8+226404.100.1.1 1554206332 installed <13>Apr 21 04:08:07 rpmi: libXinerama-1.1.3-alt1 1369984571 installed <13>Apr 21 04:08:07 rpmi: libXcomposite-0.4.3-alt3 1297306939 installed <13>Apr 21 04:08:07 rpmi: libtinfo-devel-5.9-alt8 1456756459 installed <13>Apr 21 04:08:07 rpmi: libncurses-devel-5.9-alt8 1456756459 installed <13>Apr 21 04:08:07 rpmi: python-modules-curses-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:07 rpmi: libverto-0.2.6-alt1_6 1455633234 installed <13>Apr 21 04:08:07 rpmi: libkeyutils-1.5.10-alt0.M80P.2 p8+216694.100.6.1 1547827915 installed <13>Apr 21 04:08:07 rpmi: libcom_err-1.42.13-alt2 1449075846 installed <13>Apr 21 04:08:07 rpmi: libXmu-devel-1.1.2-alt1 1391072528 installed <13>Apr 21 04:08:08 rpmi: gcc5-c++-5.3.1-alt3.M80P.1 p8+225520.100.3.1 1553688800 installed <13>Apr 21 04:08:09 rpmi: gcc5-fortran-5.3.1-alt3.M80P.1 p8+225520.100.3.1 1553688800 installed <13>Apr 21 04:08:09 rpmi: libicu-devel-1:5.6.1-alt1.1 1458012333 installed <13>Apr 21 04:08:09 rpmi: liblapack-devel-1:3.5.0-alt1 1401382194 installed <13>Apr 21 04:08:09 rpmi: libpcre-devel-8.40-alt1 1484570205 installed <13>Apr 21 04:08:09 rpmi: libtre-devel-0.8.0-alt2.1 1334590818 installed <13>Apr 21 04:08:09 rpmi: texi2dvi-6.0-alt3 1449879498 installed <13>Apr 21 04:08:09 rpmi: libtiff-devel-4.0.3-alt1 1348347498 installed <13>Apr 21 04:08:09 rpmi: libjpeg-devel-2:1.3.1-alt0.1 1388074033 installed <13>Apr 21 04:08:09 rpmi: libreadline-devel-6.3.8-alt2 1449773803 installed <13>Apr 21 04:08:09 rpmi: bzlib-devel-1:1.0.6-alt4 1449156902 installed <13>Apr 21 04:08:09 rpmi: liblzma-devel-5.2.3-alt0.M80P.1 1502296864 installed <13>Apr 21 04:08:09 rpmi: libgio-2.52.3-alt0.M80P.1 1504533271 installed <13>Apr 21 04:08:10 rpmi: texlive-base-bin-2008.0-alt0.15.6 1449446882 installed <13>Apr 21 04:08:11 rpmi: texlive-base-2008.0-alt0.15 1300007455 installed <13>Apr 21 04:08:13 rpmi: texlive-latex-base-2008.0-alt0.15 1300007455 installed <13>Apr 21 04:08:13 rpmi: gobject-introspection-1.52.1-alt0.M80P.1 1504533480 installed <13>Apr 21 04:08:13 rpmi: libssl10-1.0.2n-alt0.M80P.1 1512766129 installed <86>Apr 21 04:08:13 groupadd[31719]: group added to /etc/group: name=_keytab, GID=499 <86>Apr 21 04:08:13 groupadd[31719]: group added to /etc/gshadow: name=_keytab <86>Apr 21 04:08:13 groupadd[31719]: new group: name=_keytab, GID=499 <13>Apr 21 04:08:13 rpmi: libkrb5-1.14.6-alt1.M80P.1 1525355673 installed <13>Apr 21 04:08:13 rpmi: texlive-font-utils-2008.0-alt0.15.6 1449446882 installed <13>Apr 21 04:08:13 rpmi: libgdk-pixbuf-2.36.11-alt0.M80P.1 1507198160 installed <13>Apr 21 04:08:13 rpmi: perl-Pod-Usage-1.68-alt1 1451923699 installed <13>Apr 21 04:08:13 rpmi: libp11-kit-0.23.8-alt1.M80P.1 1504877563 installed <86>Apr 21 04:08:13 groupadd[31760]: group added to /etc/group: name=messagebus, GID=498 <86>Apr 21 04:08:13 groupadd[31760]: group added to /etc/gshadow: name=messagebus <86>Apr 21 04:08:13 groupadd[31760]: new group: name=messagebus, GID=498 <86>Apr 21 04:08:13 useradd[31767]: new user: name=messagebus, UID=499, GID=498, home=/run/dbus, shell=/dev/null <13>Apr 21 04:08:13 rpmi: dbus-1.10.24-alt4.M80P.1 1518773282 installed <13>Apr 21 04:08:14 rpmi: libcups-2.1.0-alt2.M80P.4 p8+223280.100.1.1 1551372192 installed <13>Apr 21 04:08:14 rpmi: gobject-introspection-x11-1.52.1-alt0.M80P.1 1504533480 installed <13>Apr 21 04:08:14 rpmi: gsettings-desktop-schemas-3.24.1-alt0.M80P.1 1504768052 installed <13>Apr 21 04:08:14 rpmi: libgusb-0.2.11-alt0.M80P.1 1503526571 installed <13>Apr 21 04:08:14 rpmi: libcolord-1.3.5-alt0.M80P.1 1488875506 installed <13>Apr 21 04:08:14 rpmi: perl-Unicode-Normalize-1:5.22.3-alt0.M80P.1 1485958065 installed <13>Apr 21 04:08:14 rpmi: perl-XML-SAX-0.99-alt2 1384805188 installed <13>Apr 21 04:08:14 rpmi: libharfbuzz-1.6.3-alt0.M80P.1 1509918814 installed <13>Apr 21 04:08:14 rpmi: libfreetype-2.8-alt0.M80P.3 1505462817 installed <13>Apr 21 04:08:14 rpmi: fontconfig-2.12.6-alt1.M80P.1 1506008910 installed Updating fonts cache: <29>Apr 21 04:08:15 fontconfig: Updating fonts cache: succeeded [ DONE ] <13>Apr 21 04:08:15 rpmi: libcairo-1:1.14.4-alt1 1447005495 installed <13>Apr 21 04:08:15 rpmi: libXft-2.3.2-alt1 1409902650 installed <13>Apr 21 04:08:15 rpmi: libfreetype-devel-2.8-alt0.M80P.3 1505462817 installed <13>Apr 21 04:08:15 rpmi: fontconfig-devel-2.12.6-alt1.M80P.1 1506008910 installed <13>Apr 21 04:08:15 rpmi: libpango-1.40.14-alt0.M80P.1 1510824230 installed <13>Apr 21 04:08:15 rpmi: libcairo-gobject-1:1.14.4-alt1 1447005495 installed <13>Apr 21 04:08:15 rpmi: libpango-gir-1.40.14-alt0.M80P.1 1510824230 installed <13>Apr 21 04:08:15 rpmi: libXft-devel-2.3.2-alt1 1409902650 installed <13>Apr 21 04:08:15 rpmi: libcairo-devel-1:1.14.4-alt1 1447005495 installed <13>Apr 21 04:08:15 rpmi: libtk-8.5.9-alt3 1308047279 installed <13>Apr 21 04:08:15 rpmi: tk-8.5.9-alt3 1308047279 installed <13>Apr 21 04:08:15 rpmi: perl-Tk-804.033-alt1.1 1448484960 installed <13>Apr 21 04:08:15 rpmi: libgd2-2.0.35-alt6 1366289709 installed <13>Apr 21 04:08:15 rpmi: dvipng-1.14-alt1.qa1.1 1449176640 installed <13>Apr 21 04:08:15 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 p8+224868.100.1.1 1552412385 installed <13>Apr 21 04:08:16 rpmi: libgs-9.20-alt1.M80P.1 1494700569 installed <13>Apr 21 04:08:16 rpmi: fonts-type1-xorg-7.0.0-alt4 1188553211 installed <13>Apr 21 04:08:19 rpmi: java-1.8.0-openjdk-headless-0:1.8.0.144-alt1_1.b01jpp8.M80P.3 p8+219909.100.1.1 1548335813 installed <13>Apr 21 04:08:20 rpmi: java-1.8.0-openjdk-0:1.8.0.144-alt1_1.b01jpp8.M80P.3 p8+219909.100.1.1 1548335813 installed <13>Apr 21 04:08:21 rpmi: java-1.8.0-openjdk-devel-0:1.8.0.144-alt1_1.b01jpp8.M80P.3 p8+219909.100.1.1 1548335813 installed <13>Apr 21 04:08:21 rpmi: perl-XML-Simple-2.22-alt1 1449506808 installed <13>Apr 21 04:08:21 rpmi: icon-naming-utils-0.8.90-alt1 1236573102 installed <13>Apr 21 04:08:22 rpmi: icon-theme-adwaita-3.24.0-alt0.M80P.1 1504567873 installed <13>Apr 21 04:08:22 rpmi: dbus-tools-gui-1.10.24-alt4.M80P.1 1518773282 installed <13>Apr 21 04:08:22 rpmi: at-spi2-core-2.24.1-alt0.M80P.1 1504536015 installed <13>Apr 21 04:08:22 rpmi: at-spi2-atk-2.24.1-alt0.M80P.1 1504536077 installed <13>Apr 21 04:08:22 rpmi: libgnutls30-3.6.7-alt0.M80P.1 p8+225835.100.2.1 1554226496 installed <13>Apr 21 04:08:22 rpmi: glib-networking-2.50.0-alt1.M80P.1 1503575484 installed <13>Apr 21 04:08:22 rpmi: libsoup-2.62.2-alt0.M80P.1 1528058397 installed <13>Apr 21 04:08:22 rpmi: libsoup-gnome-2.62.2-alt0.M80P.1 1528058397 installed <13>Apr 21 04:08:22 rpmi: librest-0.8.1-alt0.M80P.1 1509920808 installed <13>Apr 21 04:08:22 rpmi: gtk-update-icon-cache-2.24.31-alt1 1473461609 installed <13>Apr 21 04:08:22 rpmi: libgdk-pixbuf-gir-2.36.11-alt0.M80P.1 1507198160 installed <86>Apr 21 04:08:22 groupadd[46322]: group added to /etc/group: name=sasl, GID=497 <86>Apr 21 04:08:22 groupadd[46322]: group added to /etc/gshadow: name=sasl <86>Apr 21 04:08:22 groupadd[46322]: new group: name=sasl, GID=497 <13>Apr 21 04:08:22 rpmi: libsasl2-3-2.1.26-alt7 1479477445 installed <13>Apr 21 04:08:22 rpmi: libldap-2.4.45-alt1.M80P.1 1513980376 installed <13>Apr 21 04:08:22 rpmi: libcurl-7.64.0-alt1 p8+220788.100.1.1 1549495393 installed <13>Apr 21 04:08:22 rpmi: libpoppler72-0.61.1-alt1.M80P.1 1524829028 installed <13>Apr 21 04:08:22 rpmi: poppler-0.61.1-alt1.M80P.1 1524829028 installed <13>Apr 21 04:08:22 rpmi: libatk-gir-2.24.0-alt0.M80P.1 1504535253 installed <13>Apr 21 04:08:22 rpmi: texlive-latex3-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:08:22 rpmi: texlive-lang-tibetan-2008.0-alt0.14 1248958512 installed <13>Apr 21 04:08:23 rpmi: texlive-lang-polish-2008.0-alt0.14 1248958512 installed <13>Apr 21 04:08:23 rpmi: texmf-latex-tipa-1.3-alt4 1246545601 installed <13>Apr 21 04:08:23 rpmi: texlive-generic-extra-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:08:23 rpmi: libdconf-0.26.1-alt0.M80P.1 1507197872 installed <13>Apr 21 04:08:23 rpmi: dconf-0.26.1-alt0.M80P.1 1507197872 installed <13>Apr 21 04:08:23 rpmi: libgtk+3-schemas-3.22.26-alt0.M80P.1 1510825424 installed <13>Apr 21 04:08:23 rpmi: libpolkit-0.113-alt2 1469643478 installed <86>Apr 21 04:08:23 groupadd[47764]: group added to /etc/group: name=colord, GID=496 <86>Apr 21 04:08:23 groupadd[47764]: group added to /etc/gshadow: name=colord <86>Apr 21 04:08:23 groupadd[47764]: new group: name=colord, GID=496 <86>Apr 21 04:08:23 useradd[47771]: new user: name=colord, UID=498, GID=496, home=/var/colord, shell=/dev/null <13>Apr 21 04:08:23 rpmi: colord-1.3.5-alt0.M80P.1 1488875506 installed <13>Apr 21 04:08:23 rpmi: libjson-glib-1.2.8-alt0.M80P.1 1489956779 installed <13>Apr 21 04:08:24 rpmi: libgtk+3-3.22.26-alt0.M80P.1 1510825302 installed <13>Apr 21 04:08:24 rpmi: libgtk+3-gir-3.22.26-alt0.M80P.1 1510825302 installed <13>Apr 21 04:08:24 rpmi: perl-podlators-4.07-alt1 1458574366 installed <13>Apr 21 04:08:24 rpmi: perl-unicore-1:5.22.3-alt0.M80P.1 1485958186 installed <13>Apr 21 04:08:24 rpmi: perl-XML-LibXML-2.0124-alt1 1458750523 installed <13>Apr 21 04:08:24 rpmi: libp11-kit-trust-0.23.8-alt1.M80P.1 1504877563 installed <13>Apr 21 04:08:24 rpmi: dbus-tools-1.10.24-alt4.M80P.1 1518773282 installed <13>Apr 21 04:08:24 rpmi: libcurl-devel-7.64.0-alt1 p8+220788.100.1.1 1549495393 installed <13>Apr 21 04:08:24 rpmi: tk-devel-8.5.9-alt3 1308047279 installed <13>Apr 21 04:08:24 rpmi: makeinfo-6.0-alt3 1449879498 installed <13>Apr 21 04:08:24 rpmi: python3-base-3.5.4-alt2.M80P.1 1527753911 installed <13>Apr 21 04:08:24 rpmi: python3-module-six-1.10.0-alt7 1496087616 installed <13>Apr 21 04:08:24 rpmi: python-modules-compiler-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:24 rpmi: python3-module-cycler-0.10.0-alt1 1493854024 installed <13>Apr 21 04:08:24 rpmi: python3-module-dateutil-2.4.2-alt1.git20150728.1.1 1458152500 installed <13>Apr 21 04:08:24 rpmi: python3-module-certifi-2015.04.28-alt1.1 1457893771 installed <13>Apr 21 04:08:24 rpmi: python3-module-cssselect-0.9.1-alt1.1 1457858257 installed <13>Apr 21 04:08:24 rpmi: python3-module-webencodings-0.5.1-alt0.M80P.1 1507185481 installed <13>Apr 21 04:08:24 rpmi: python3-module-pyparsing-2.0.3-alt1.1 1458039018 installed <13>Apr 21 04:08:24 rpmi: python3-module-z3c-3.0.0-alt2.a2.dev0.git20130313.1.1.1 1460417103 installed <13>Apr 21 04:08:24 rpmi: python3-module-zc-1.0.0-alt6.2 1458024144 installed <13>Apr 21 04:08:25 rpmi: ghostscript-common-9.20-alt1.M80P.1 1494700614 installed <13>Apr 21 04:08:25 rpmi: ghostscript-classic-9.20-alt1.M80P.1 1494700569 installed <13>Apr 21 04:08:25 rpmi: latex2html-2012-alt1 1450368036 installed <13>Apr 21 04:08:25 rpmi: python3-3.5.4-alt2.M80P.1 1527753911 installed <13>Apr 21 04:08:25 rpmi: python-modules-email-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:25 rpmi: python3-module-pycares-0.6.3-alt1.1.1 1459598195 installed <13>Apr 21 04:08:25 rpmi: python3-module-pycairo-1.13.3-alt0.M80P.1 1504561359 installed <13>Apr 21 04:08:25 rpmi: python3-module-pygobject3-3.24.1-alt1.M80P.1 1504561842 installed <13>Apr 21 04:08:25 rpmi: rpm-build-python3-0.1.10.10-alt1.M80P.1 1530521451 installed <13>Apr 21 04:08:26 rpmi: python3-module-numpy-1:1.12.1-alt0.M80P.1 1496160663 installed <13>Apr 21 04:08:26 rpmi: python3-module-zope-3.3.0-alt8.4 1458261152 installed <13>Apr 21 04:08:26 rpmi: python3-module-lxml-4.0.0-alt0.M80P.1 1507163741 installed <13>Apr 21 04:08:26 rpmi: python3-module-tornado-4.2.1-alt2.M80P.1 1496088637 installed <13>Apr 21 04:08:26 rpmi: python3-module-numpy-testing-1:1.12.1-alt0.M80P.1 1496160663 installed <13>Apr 21 04:08:26 rpmi: python3-module-zope.interface-4.1.3-alt1.dev0.git20150601.4 1459629874 installed <13>Apr 21 04:08:26 rpmi: python3-module-html5lib-1:0.999999999-alt1.M80P.2 1507185603 installed <13>Apr 21 04:08:26 rpmi: python-modules-unittest-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:26 rpmi: python-modules-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:26 rpmi: python-modules-xml-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python3-module-matplotlib-2.0.0-alt3.M80P.1 1498628280 installed <13>Apr 21 04:08:27 rpmi: python-modules-encodings-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python3-module-javapackages-1:4.6.0-alt9_12jpp8.1.1 1460387057 installed <13>Apr 21 04:08:27 rpmi: rpm-build-java-1:4.6.0-alt9_12jpp8.1.1 1460387057 installed <13>Apr 21 04:08:27 rpmi: python-modules-hotshot-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python-modules-bsddb-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python-modules-ctypes-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python-modules-multiprocessing-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python-modules-logging-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: python-dev-2.7.11-alt6.M80P.1 1527682470 installed <13>Apr 21 04:08:27 rpmi: glib2-devel-2.52.3-alt0.M80P.1 1504533271 installed <13>Apr 21 04:08:27 rpmi: python3-module-matplotlib-gtk3-2.0.0-alt3.M80P.1 1498628280 installed <13>Apr 21 04:08:27 rpmi: python3-module-matplotlib-cairo-2.0.0-alt3.M80P.1 1498628280 installed <13>Apr 21 04:08:27 rpmi: libpango-devel-1.40.14-alt0.M80P.1 1510824230 installed <13>Apr 21 04:08:27 rpmi: java-devel-default-1.7.0-alt1 1454012839 installed <13>Apr 21 04:08:29 rpmi: texlive-fonts-recommended-2008.0-alt0.15 1300007455 installed <13>Apr 21 04:08:38 rpmi: texlive-latex-recommended-2008.0-alt0.15 1300007455 installed <13>Apr 21 04:08:38 rpmi: texlive-generic-recommended-2008.0-alt0.15 1300007455 installed <13>Apr 21 04:08:39 rpmi: texlive-math-extra-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:08:39 rpmi: texlive-lang-french-2008.0-alt0.14 1248958512 installed <13>Apr 21 04:08:39 rpmi: texlive-extra-utils-2008.0-alt0.15.6 1449446882 installed <13>Apr 21 04:08:39 rpmi: texlive-lang-german-2008.0-alt0.14 1248958512 installed <13>Apr 21 04:08:39 rpmi: texlive-lang-cyrillic-2008.0-alt0.14 1248958512 installed <13>Apr 21 04:08:39 rpmi: texmf-latex-xcolor-2.06-alt3 1244802289 installed <13>Apr 21 04:08:40 rpmi: texmf-pgf-3.0.1-alt1 1439012888 installed <13>Apr 21 04:08:46 rpmi: texlive-fonts-extra-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:08:56 rpmi: texlive-pstricks-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:08:56 rpmi: texlive-games-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:08:56 rpmi: texmf-latex-obsolete-0.1-alt1 1244748792 installed <13>Apr 21 04:08:56 rpmi: texlive-lang-arab-2008.0-alt0.14 1248958512 installed <13>Apr 21 04:08:57 rpmi: texlive-xetex-2008.0-alt0.15.6 1449446882 installed <13>Apr 21 04:08:57 rpmi: texmf-latex-beamer-3.36-alt4 1451249538 installed <13>Apr 21 04:08:59 rpmi: texlive-publishers-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:09:00 rpmi: texlive-pictures-2008.0-alt0.15 1300007455 installed <13>Apr 21 04:09:00 rpmi: texlive-science-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:09:01 rpmi: texlive-humanities-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:09:09 rpmi: texlive-latex-extra-2008.0-alt0.16 1300008623 installed <13>Apr 21 04:09:09 rpmi: texlive-bibtex-extra-2008.0-alt0.16 1300008623 installed Installing R-base-3.4.3-alt0.M80P.1.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.27697 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf R-3.4.3 + echo 'Source #0 (R-3.4.3.tar):' Source #0 (R-3.4.3.tar): + /bin/tar -xf /usr/src/RPM/SOURCES/R-3.4.3.tar + cd R-3.4.3 + /bin/chmod -c -Rf u+rwX,go-w . + echo 'Patch #0 (R-3.4.3-alt0.M80P.1.patch):' Patch #0 (R-3.4.3-alt0.M80P.1.patch): + /usr/bin/patch -p1 patching file .gear/rules patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0 patching file .gear/tags/9bcb4bdb4dd1185d3f43ac2d1ba0d8a70921a4e0 patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5 patching file .gear/tags/a8802667f7d1597d2cd5442d00d4d4773505446e patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020 patching file .gear/tags/dbe24e8137437d3688e1d77cf1b67279d3099cea patching file .gear/tags/ebdb5ee7ba9a5499c21aadcfee3318a7d6d52061 patching file .gear/tags/f600e7641c9fbf40a0abc5b1cdd67c703376e847 patching file .gear/tags/fdd01de5a3b9e7e6d41e1f4f9db33a99b6973818 patching file .gear/tags/list patching file R-base.spec patching file src/extra/blas/Makefile.in patching file src/extra/xdr/Makefile.in patching file src/library/base/R/datetime.R patching file tests/reg-tests-1c.R patching file tests/reg-tests-1d.R + rm src/extra/blas/blas.f src/extra/blas/cmplxblas.f src/modules/lapack/cmplx.f src/modules/lapack/dlamch.f src/modules/lapack/dlapack.f src/modules/lapack/vecLibg95f.f + exit 0 Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.60655 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.4.3 + export lt_cv_prog_cc_static_works=no ac_cv_path_R_ZIPCMD=zip ac_cv_path_R_UNZIPCMD=unzip ac_cv_path_R_BROWSER=firefox ac_cv_path_R_PDFVIEWER=evince 'ac_cv_path_PAGER=less -isR' ac_cv_prog_R_PRINTCMD=lpr + lt_cv_prog_cc_static_works=no + ac_cv_path_R_ZIPCMD=zip + ac_cv_path_R_UNZIPCMD=unzip + ac_cv_path_R_BROWSER=firefox + ac_cv_path_R_PDFVIEWER=evince + ac_cv_path_PAGER='less -isR' + ac_cv_prog_R_PRINTCMD=lpr + CFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing' + export CFLAGS + CXXFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing' + export CXXFLAGS + FFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing' + export FFLAGS + '[' -n '' ']' ++ printf %s '-pipe -Wall -g -O2 -fno-strict-aliasing' ++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g' + ASFLAGS= + export ASFLAGS + export lt_cv_deplibs_check_method=pass_all + lt_cv_deplibs_check_method=pass_all + xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess + sort -u + xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n' + xargs -ri dirname -- '{}' + readlink -e -- ./configure + ./configure --build=x86_64-alt-linux --host=x86_64-alt-linux --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/lib --localstatedir=/var/lib --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-dependency-tracking --without-included-gettext --enable-prebuilt-html --enable-R-shlib --with-x --disable-rpath --with-system-tre --with-gnu-ld --with-blas=openblas --with-lapack=lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh '--libdir=${prefix}/lib64' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-3.4' configure: WARNING: unrecognized options: --disable-dependency-tracking checking build system type... x86_64-alt-linux-gnu checking host system type... x86_64-alt-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking whether ln -s works... yes checking for bison... bison -y checking for ar... ar checking for a BSD-compatible install... /bin/install -c checking for sed... /bin/sed checking for which... /usr/bin/which checking for less... (cached) less -isR checking for gtar... /usr/bin/gtar checking for tex... /usr/bin/tex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeindex... /usr/bin/makeindex checking for texi2any... /usr/bin/texi2any checking whether texi2any version is at least 5.1... yes checking for ginstall-info... no checking for install-info... no checking for texi2dvi... /usr/bin/texi2dvi checking for kpsewhich... /usr/bin/kpsewhich checking for latex inconsolata package... missing configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally checking for unzip... (cached) unzip checking for zip... (cached) zip checking for gzip... /bin/gzip checking for bzip2... /bin/bzip2 checking for firefox... (cached) firefox using default browser ... firefox checking for acroread... (cached) evince checking for notangle... false checking for realpath... /usr/bin/realpath checking for pkg-config... /usr/bin/pkg-config checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-alt-linux-gcc accepts -g... yes checking for x86_64-alt-linux-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... x86_64-alt-linux-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether x86_64-alt-linux-gcc needs -traditional... no checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking how to run the C preprocessor... x86_64-alt-linux-gcc -E checking for f95... f95 checking for x86_64-alt-linux-g77... (cached) f95 checking whether we are using the GNU Fortran 77 compiler... yes checking whether f95 accepts -g... yes checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-alt-linux-g++ accepts -g... yes checking whether x86_64-alt-linux-g++ -pipe -Wall -g -O2 -fno-strict-aliasing can compile C++ code... yes checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether x86_64-alt-linux-gcc accepts -fvisibility... yes checking whether f95 accepts -fvisibility... yes checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc checking whether we are using the GNU Objective C compiler... no checking whether x86_64-alt-linux-gcc accepts -g... no checking for Objective C++ compiler... trying some possibilities checking whether x86_64-alt-linux-g++ can compile ObjC++... no no working ObjC++ compiler found checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-alt-linux-gnu file names to x86_64-alt-linux-gnu format... func_convert_file_noop checking how to convert x86_64-alt-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for x86_64-alt-linux-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... (cached) pass_all checking for x86_64-alt-linux-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-alt-linux-ar... (cached) ar checking for archiver @FILE support... @ checking for x86_64-alt-linux-strip... no checking for strip... strip checking for x86_64-alt-linux-ranlib... no checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from x86_64-alt-linux-gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-alt-linux-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-alt-linux-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-alt-linux-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-alt-linux-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-alt-linux-gcc static flag -static works... no checking if x86_64-alt-linux-gcc supports -c -o file.o... yes checking if x86_64-alt-linux-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E checking for ld used by x86_64-alt-linux-g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-alt-linux-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-alt-linux-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-alt-linux-g++ static flag -static works... no checking if x86_64-alt-linux-g++ supports -c -o file.o... yes checking if x86_64-alt-linux-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for f95 option to produce PIC... -fPIC checking if f95 PIC flag -fPIC works... yes checking if f95 static flag -static works... no checking if f95 supports -c -o file.o... yes checking if f95 supports -c -o file.o... (cached) yes checking whether the f95 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking whether rl_callback_sigcleanup exists and is declared... no checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking glob.h usability... yes checking glob.h presence... yes checking for glob.h... yes checking grp.h usability... yes checking grp.h presence... yes checking for grp.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for strings.h... (cached) yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking dl.h usability... no checking dl.h presence... no checking for dl.h... no checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking floatingpoint.h usability... no checking floatingpoint.h presence... no checking for floatingpoint.h... no checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking stdalign.h usability... yes checking stdalign.h presence... yes checking for stdalign.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking return type of signal handlers... void checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for x86_64-alt-linux-gcc option to accept ISO C99... none needed checking for x86_64-alt-linux-gcc option to accept ISO Standard C... (cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether x86_64-alt-linux-gcc supports -c -o FILE.lo... yes checking for x86_64-alt-linux-gcc option to support OpenMP... unsupported checking how to get verbose linking output from f95... -v checking for Fortran 77 libraries of f95... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from x86_64-alt-linux-gcc... -v checking for C libraries of x86_64-alt-linux-gcc... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../.. -lgcc_s checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking whether f95 appends underscores to external names... yes checking whether f95 appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether f95 and x86_64-alt-linux-gcc agree on int and double... yes checking whether f95 and x86_64-alt-linux-gcc agree on double complex... yes checking for f95 option to support OpenMP... unsupported checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes checking for x86_64-alt-linux-g++ option to support OpenMP... unsupported checking whether we can compute ObjC Make dependencies... no checking for ObjC runtime library... checking whether x86_64-alt-linux-gcc accepts -fobjc-exceptions... no checking whether C runtime needs -D__NO_MATH_INLINES... no checking for xmkmf... no checking whether x86_64-alt-linux-g++ supports C++98 features by default... yes checking whether x86_64-alt-linux-g++ supports C++11 features by default... no checking whether x86_64-alt-linux-g++ supports C++11 features with -std=gnu++11... yes checking whether x86_64-alt-linux-g++ supports C++14 features by default... no checking whether x86_64-alt-linux-g++ supports C++14 features with -std=gnu++14... yes checking whether x86_64-alt-linux-g++ supports C++17 features by default... no checking whether x86_64-alt-linux-g++ supports C++17 features with -std=gnu++17... no checking whether x86_64-alt-linux-g++ supports C++17 features with -std=gnu++1z... no checking whether x86_64-alt-linux-g++ supports C++17 features with -std=c++17... no checking whether x86_64-alt-linux-g++ supports C++17 features with -std=c++1z... no configure: No compiler with C++17 support was found checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rint exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking sunmath.h usability... no checking sunmath.h presence... no checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... yes checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... none required checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... yes checking whether mktime works correctly outside 1902-2037... yes checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_ in -lopenblas... yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for dpstrf_... no checking for dpstrf_ in -llapack... yes checking iconv.h usability... yes checking iconv.h presence... yes checking for iconv.h... yes checking for iconv... yes checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes checking for iconvlist... no checking for iconv... yes checking for iconv declaration... extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether wcstod exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether iswblank exists and is declared... yes checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes checking for wctrans_t... yes checking for mbstate_t... yes checking for ICU... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for XtToolkitInitialize in -lXt... yes using X11 ... yes checking for KeySym... yes checking X11/Xmu/Atoms.h usability... yes checking X11/Xmu/Atoms.h presence... yes checking for X11/Xmu/Atoms.h... yes checking for XmuInternAtom in -lXmu... yes checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for /usr/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh checking for /usr/lib64/tkConfig.sh... /usr/lib64/tkConfig.sh checking tcl.h usability... yes checking tcl.h presence... yes checking for tcl.h... yes checking tk.h usability... yes checking tk.h presence... yes checking for tk.h... yes checking whether compiling/linking Tcl/Tk code works... yes checking for BSD networking... yes checking rpc/types.h usability... yes checking rpc/types.h presence... yes checking for rpc/types.h... yes checking for rpc/xdr.h... yes checking for XDR support... yes checking for inflateInit2_ in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.2.5... yes checking whether zlib support suffices... yes checking mmap support for zlib... yes checking for BZ2_bzlibVersion in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking if bzip2 version >= 1.0.6... yes checking whether bzip2 support suffices... yes checking for lzma_version_number in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking if lzma version >= 5.0.3... yes checking for pcre_fullinfo in -lpcre... yes checking pcre.h usability... no checking pcre.h presence... no checking for pcre.h... no checking pcre/pcre.h usability... yes checking pcre/pcre.h presence... yes checking for pcre/pcre.h... yes checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... yes checking if PCRE version >= 8.32... yes checking whether PCRE support suffices... yes checking for tre_regncompb in -ltre... no checking for curl-config... /usr/bin/curl-config checking libcurl version ... 7.64.0-DEV checking curl/curl.h usability... yes checking curl/curl.h presence... yes checking for curl/curl.h... yes checking if libcurl is version 7 and >= 7.22.0... yes checking if libcurl supports https... yes checking if jpeglib version >= 6b... yes checking for jpeg_destroy_compress in -ljpeg... yes checking if libpng version >= 1.2.7... yes checking for png_create_write_struct in -lpng... yes checking tiffio.h usability... yes checking tiffio.h presence... yes checking for tiffio.h... yes checking for TIFFOpen in -ltiff... yes checking whether leap seconds are treated according to POSIX... yes checking for inline... inline checking for sys/time.h... (cached) yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for struct stat.st_atim.tv_nsec... yes checking whether struct stat.st_atim is of type struct timespec... yes checking for setitimer... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking whether KERN_USRSTACK sysctl is supported... no checking for visible __lib_stack_end... yes checking for lpr... (cached) lpr checking for paperconf... /usr/bin/paperconf checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran checking whether we are using the GNU Fortran compiler... yes checking whether x86_64-alt-linux-gfortran accepts -g... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for x86_64-alt-linux-gfortran option to produce PIC... -fPIC checking if x86_64-alt-linux-gfortran PIC flag -fPIC works... yes checking if x86_64-alt-linux-gfortran static flag -static works... no checking if x86_64-alt-linux-gfortran supports -c -o file.o... yes checking if x86_64-alt-linux-gfortran supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for x86_64-alt-linux-gfortran option to support OpenMP... unsupported checking for recommended packages... yes checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for x86_64-alt-linux-ranlib... ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... yes checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.0.4.0.14.8, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... no using as R_SHELL for scripts ... /bin/sh configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/f77_f2c config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --disable-dependency-tracking R is now configured for x86_64-alt-linux-gnu Source directory: . Installation directory: /usr C compiler: x86_64-alt-linux-gcc -pipe -Wall -g -O2 -fno-strict-aliasing Fortran 77 compiler: f95 -pipe -Wall -g -O2 -fno-strict-aliasing Default C++ compiler: x86_64-alt-linux-g++ -pipe -Wall -g -O2 -fno-strict-aliasing C++98 compiler: x86_64-alt-linux-g++ -pipe -Wall -g -O2 -fno-strict-aliasing C++11 compiler: x86_64-alt-linux-g++ -std=gnu++11 -pipe -Wall -g -O2 -fno-strict-aliasing C++14 compiler: x86_64-alt-linux-g++ -std=gnu++14 -pipe -Wall -g -O2 -fno-strict-aliasing C++17 compiler: Fortran 90/95 compiler: x86_64-alt-linux-gfortran -g -O2 Obj-C compiler: x86_64-alt-linux-gcc Interfaces supported: X11, tcltk External libraries: readline, BLAS(OpenBLAS), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, static HTML Capabilities skipped: Options not enabled: shared BLAS, memory profiling Recommended packages: yes configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally + '[' -n '' ']' + NPROCS=8 + make -j8 make: Entering directory `/usr/src/RPM/BUILD/R-3.4.3' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/m4' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/m4' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tools' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tools' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/doc' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/doc/html' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc/html' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/doc/manual' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc/manual' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/etc' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/etc' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/share' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/share' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/scripts' creating src/scripts/R.fe make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/scripts' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/scripts' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/include' mkdir -p -- ../../include make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/include/R_ext' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/include' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra/tre' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra/tre' making regcomp.d from regcomp.c making regerror.d from regerror.c making regexec.d from regexec.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c making tre-match-backtrack.d from tre-match-backtrack.c making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-parse.d from tre-parse.c making tre-stack.d from tre-stack.c making xmalloc.d from xmalloc.c make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra/tre' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o ranlib libtre.a make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra/tre' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra/tre' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/extra' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c interv.c -o interv.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c maxcol.c -o maxcol.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pretty.c -o pretty.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c uncmin.c -o uncmin.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dchdc.f -o dchdc.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpbfa.f -o dpbfa.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpbsl.f -o dpbsl.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpoco.f -o dpoco.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpodi.f -o dpodi.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpofa.f -o dpofa.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dposl.f -o dposl.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrdc.f -o dqrdc.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrls.f -o dqrls.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrsl.f -o dqrsl.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dqrutl.f -o dqrutl.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dsvdc.f -o dsvdc.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtrco.f -o dtrco.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtrsl.f -o dtrsl.o ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/appl' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/appl' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making pt.d from pt.c making dt.d from dt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dnbinom.d from dnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making qnf.d from qnf.c making pnt.d from pnt.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mlutils.c -o mlutils.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c d1mach.c -o d1mach.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c i1mach.c -o i1mach.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fmax2.c -o fmax2.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fmin2.c -o fmin2.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fprec.c -o fprec.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fround.c -o fround.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ftrunc.c -o ftrunc.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sign.c -o sign.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fsign.c -o fsign.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c imax2.c -o imax2.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c imin2.c -o imin2.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chebyshev.c -o chebyshev.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c log1p.c -o log1p.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c expm1.c -o expm1.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lgammacor.c -o lgammacor.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gammalims.c -o gammalims.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stirlerr.c -o stirlerr.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bd0.c -o bd0.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gamma.c -o gamma.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lgamma.c -o lgamma.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c beta.c -o beta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lbeta.c -o lbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c polygamma.c -o polygamma.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cospi.c -o cospi.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_i.c -o bessel_i.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_j.c -o bessel_j.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_k.c -o bessel_k.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bessel_y.c -o bessel_y.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c choose.c -o choose.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c snorm.c -o snorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sexp.c -o sexp.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgamma.c -o dgamma.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pgamma.c -o pgamma.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qgamma.c -o qgamma.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rgamma.c -o rgamma.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dbeta.c -o dbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pbeta.c -o pbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qbeta.c -o qbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rbeta.c -o rbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dunif.c -o dunif.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c punif.c -o punif.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qunif.c -o qunif.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c runif.c -o runif.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnorm.c -o dnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnorm.c -o pnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnorm.c -o qnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rnorm.c -o rnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dlnorm.c -o dlnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plnorm.c -o plnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qlnorm.c -o qlnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlnorm.c -o rlnorm.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c df.c -o df.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pf.c -o pf.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qf.c -o qf.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rf.c -o rf.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnf.c -o dnf.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dt.c -o dt.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pt.c -o pt.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qt.c -o qt.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rt.c -o rt.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnt.c -o dnt.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dchisq.c -o dchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pchisq.c -o pchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qchisq.c -o qchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rchisq.c -o rchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rnchisq.c -o rnchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dbinom.c -o dbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pbinom.c -o pbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qbinom.c -o qbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rbinom.c -o rbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rmultinom.c -o rmultinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dcauchy.c -o dcauchy.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pcauchy.c -o pcauchy.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qcauchy.c -o qcauchy.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rcauchy.c -o rcauchy.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dexp.c -o dexp.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pexp.c -o pexp.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qexp.c -o qexp.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rexp.c -o rexp.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgeom.c -o dgeom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pgeom.c -o pgeom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qgeom.c -o qgeom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rgeom.c -o rgeom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dhyper.c -o dhyper.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c phyper.c -o phyper.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qhyper.c -o qhyper.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rhyper.c -o rhyper.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnbinom.c -o dnbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnbinom.c -o pnbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnbinom.c -o qnbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rnbinom.c -o rnbinom.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpois.c -o dpois.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ppois.c -o ppois.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qpois.c -o qpois.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpois.c -o rpois.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dweibull.c -o dweibull.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pweibull.c -o pweibull.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qweibull.c -o qweibull.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rweibull.c -o rweibull.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dlogis.c -o dlogis.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plogis.c -o plogis.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qlogis.c -o qlogis.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlogis.c -o rlogis.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnchisq.c -o dnchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnchisq.c -o pnchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnchisq.c -o qnchisq.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dnbeta.c -o dnbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnbeta.c -o pnbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnbeta.c -o qnbeta.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnf.c -o pnf.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pnt.c -o pnt.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnf.c -o qnf.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qnt.c -o qnt.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ptukey.c -o ptukey.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qtukey.c -o qtukey.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c toms708.c -o toms708.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c wilcox.c -o wilcox.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c signrank.c -o signrank.o ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/nmath' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/nmath' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rembedded.c -o Rembedded.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dynload.c -o dynload.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c system.c -o system.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sys-unix.c -o sys-unix.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sys-std.c -o sys-std.o x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c X11.c -o X11.o ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -Wall -g -O2 -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-3.4.3"' \ -o Rscript ./Rscript.c make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/unix' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making RNG.d from RNG.c making Renviron.d from Renviron.c making agrep.d from agrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making context.d from context.c making connections.d from connections.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making random.d from random.c making radixsort.d from radixsort.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making unique.d from unique.c making times.d from times.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rdynload.c -o Rdynload.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Renviron.c -o Renviron.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c RNG.c -o RNG.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agrep.c -o agrep.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c apply.c -o apply.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c arithmetic.c -o arithmetic.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c array.c -o array.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c attrib.c -o attrib.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bind.c -o bind.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c builtin.c -o builtin.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c character.c -o character.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coerce.c -o coerce.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c complex.c -o complex.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c connections.c -o connections.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c context.c -o context.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cum.c -o cum.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dcf.c -o dcf.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c datetime.c -o datetime.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c debug.c -o debug.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c deparse.c -o deparse.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dotcode.c -o dotcode.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dounzip.c -o dounzip.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dstruct.c -o dstruct.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c duplicate.c -o duplicate.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c edit.c -o edit.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c engine.c -o engine.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c envir.c -o envir.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c errors.c -o errors.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c eval.c -o eval.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gevents.c -o gevents.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gram.c -o gram.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gram-ex.c -o gram-ex.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c grep.c -o grep.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c identical.c -o identical.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c inlined.c -o inlined.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c inspect.c -o inspect.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c internet.c -o internet.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c iosupport.c -o iosupport.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lapack.c -o lapack.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c list.c -o list.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c localecharset.c -o localecharset.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c logic.c -o logic.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c main.c -o main.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mapply.c -o mapply.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c match.c -o match.o main.c: In function 'dummy_ii': main.c:1669:12: warning: function returns address of local variable [-Wreturn-local-addr] return (uintptr_t) ⅈ ^ x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c memory.c -o memory.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c names.c -o names.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c objects.c -o objects.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c options.c -o options.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c paste.c -o paste.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c platform.c -o platform.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot.c -o plot.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot3d.c -o plot3d.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plotmath.c -o plotmath.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c print.c -o print.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c printarray.c -o printarray.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c printvector.c -o printvector.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c printutils.c -o printutils.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qsort.c -o qsort.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c radixsort.c -o radixsort.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c random.c -o random.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c raw.c -o raw.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c registration.c -o registration.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c relop.c -o relop.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlocale.c -o rlocale.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c saveload.c -o saveload.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c scan.c -o scan.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c seq.c -o seq.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c serialize.c -o serialize.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sort.c -o sort.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c source.c -o source.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c split.c -o split.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sprintf.c -o sprintf.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c startup.c -o startup.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c subassign.c -o subassign.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c subscript.c -o subscript.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c subset.c -o subset.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c summary.c -o summary.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sysutils.c -o sysutils.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c times.c -o times.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c unique.c -o unique.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c version.c -o version.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_cntrlify.c -o g_cntrlify.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_fontdb.c -o g_fontdb.o x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c xxxpr.f -o xxxpr.o x86_64-alt-linux-gcc -shared -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lopenblas -lgfortran -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-3.4.3/bin/exec mkdir -p -- /usr/src/RPM/BUILD/R-3.4.3/lib make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rmain.c -o Rmain.o x86_64-alt-linux-gcc -Wl,--export-dynamic -L../../lib -L/usr/local/lib64 -o R.bin Rmain.o -lR make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/main' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/internet' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/lapack' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/X11' making Lapack.d from Lapack.c making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c making libcurl.d from libcurl.c making internet.d from internet.c making nanoftp.d from nanoftp.c making nanohttp.d from nanohttp.c making sock.d from sock.c making sockconn.d from sockconn.c make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/lapack' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Lapack.c -o Lapack.o make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng15 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devX11.c -o devX11.o x86_64-alt-linux-gcc -I/usr/include/libpng15 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rotated.c -o rotated.o x86_64-alt-linux-gcc -I/usr/include/libpng15 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rbitmap.c -o rbitmap.o x86_64-alt-linux-gcc -I/usr/include/libpng15 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dataentry.c -o dataentry.o make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanoftp.c -o nanoftp.o x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o lapack.so Lapack.o -lR -llapack -lopenblas -lgfortran -lm -lquadmath make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/lapack' mkdir -p -- /usr/src/RPM/BUILD/R-3.4.3/modules make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/lapack' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/lapack' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/lapack' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanohttp.c -o nanohttp.o x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/internet' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/internet' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/internet' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/internet' x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng15 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/X11' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/X11' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/X11' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules/X11' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/modules' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' mkdir -p -- ../../library make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/profile' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/translations' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/translations' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/translations' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' building package 'base' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c text.c -o text.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rmd5.c -o Rmd5.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c md5.c -o md5.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c signals.c -o signals.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c install.c -o install.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c getfmts.c -o getfmts.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c http.c -o http.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gramLatex.c -o gramLatex.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gramRd.c -o gramRd.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/compiler' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/compiler' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/compiler' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' byte-compiling package 'base' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tools' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils/src' making init.d from init.c making io.d from io.c making sock.d from sock.c making size.d from size.c making stubs.d from stubs.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o making utils.d from utils.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c io.c -o io.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c size.c -o size.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sock.c -o sock.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stubs.c -o stubs.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c utils.c -o utils.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/utils' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src' making axis_scales.d from axis_scales.c making chull.d from chull.c making devices.d from devices.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making devCairo.d from devCairo.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c axis_scales.c -o axis_scales.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chull.c -o chull.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stubs.c -o stubs.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devCairo.c -o devCairo.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devPicTeX.c -o devPicTeX.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devPS.c -o devPS.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c devQuartz.c -o devQuartz.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[7]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[8]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src/cairo' make[9]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src/cairo' x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cairoBM.c -o cairoBM.o x86_64-alt-linux-gcc -shared -L../../../../../lib -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng15 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -L../../../../../lib -lR -lm make[9]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src/cairo' make[8]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src/cairo' make[7]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src/cairo' make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grDevices' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c making stem.d from stem.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c base.c -o base.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c par.c -o par.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot.c -o plot.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c plot3d.c -o plot3d.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stem.c -o stem.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/graphics' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making bandwidths.d from bandwidths.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making dblcen.d from dblcen.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fourier.d from fourier.c making fft.d from fft.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making rcont.d from rcont.c making zeroin.d from zeroin.c making influence.d from influence.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c kmeans.c -o kmeans.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ansari.c -o ansari.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bandwidths.c -o bandwidths.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chisqsim.c -o chisqsim.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fexact.c -o fexact.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c kendall.c -o kendall.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ks.c -o ks.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c line.c -o line.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c smooth.c -o smooth.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c prho.c -o prho.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c swilk.c -o swilk.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ksmooth.c -o ksmooth.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c loessc.c -o loessc.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c monoSpl.c -o monoSpl.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c isoreg.c -o isoreg.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Srunmed.c -o Srunmed.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dblcen.c -o dblcen.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c distance.c -o distance.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c hclust-utils.c -o hclust-utils.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nls.c -o nls.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rWishart.c -o rWishart.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c HoltWinters.c -o HoltWinters.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c PPsum.c -o PPsum.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c arima.c -o arima.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c burg.c -o burg.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c filter.c -o filter.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mAR.c -o mAR.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pacf.c -o pacf.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c starma.c -o starma.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c port.c -o port.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c family.c -o family.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sbart.c -o sbart.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c approx.c -o approx.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c loglin.c -o loglin.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lowess.c -o lowess.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c massdist.c -o massdist.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c splines.c -o splines.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lm.c -o lm.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c complete_cases.c -o complete_cases.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cov.c -o cov.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c deriv.c -o deriv.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fft.c -o fft.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fourier.c -o fourier.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c model.c -o model.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c optimize.c -o optimize.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c random.c -o random.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c distn.c -o distn.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c zeroin.c -o zeroin.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rcont.c -o rcont.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c influence.c -o influence.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bsplvd.f -o bsplvd.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bvalue.f -o bvalue.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bvalus.f -o bvalus.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c loessf.f -o loessf.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ppr.f -o ppr.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c qsbart.f -o qsbart.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sgram.f -o sgram.o loessf.f:59:14: j=DBLE(j)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1893:14: m=DBLE(l+u)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1398:20: i=phi(pi(ii)) 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:927:12: lg=DBLE(lg)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:522:22: if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1204:13: ifloor=x 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:834:22: if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1582:18: i1=dble((d+2)*(d+1))/2.d0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sinerp.f -o sinerp.o loessf.f:472:25: subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s) 1 Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument] loessf.f:472:39: subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s) 1 Warning: Unused dummy argument 'nc' at (1) [-Wunused-dummy-argument] loessf.f:827:31: subroutine ehg197(deg,tau,d,f,dk,trl) 1 Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument] loessf.f:1984:31: subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 1 Warning: Unused dummy argument 'kappa' at (1) [-Wunused-dummy-argument] loessf.f:1984:47: subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 1 Warning: Unused dummy argument 'nv' at (1) [-Wunused-dummy-argument] loessf.f:1984:53: subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 1 Warning: Unused dummy argument 'nvmax' at (1) [-Wunused-dummy-argument] loessf.f:1497:50: subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1497:53: subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1648:30: subroutine lowese(iv,liv,lv,wv,m,z,s) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1648:33: subroutine lowese(iv,liv,lv,wv,m,z,s) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1667:39: subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1667:42: subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1699:30: subroutine lowesl(iv,liv,lv,wv,m,z,l) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1699:33: subroutine lowesl(iv,liv,lv,wv,m,z,l) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1721:33: subroutine lowesr(yy,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1721:36: subroutine lowesr(yy,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sslvrg.f -o sslvrg.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stxwx.f -o stxwx.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c hclust.f -o hclust.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c kmns.f -o kmns.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c eureka.f -o eureka.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stl.f -o stl.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -ffloat-store -c portsrc.f -o portsrc.o f95 -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lminfl.f -o lminfl.o portsrc.f:6340:0: * MAXLST,NCOMP,NUMINC,NUMLST,NUMORD,NUMWGT ^ Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:6339:0: INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC, ^ Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:5328:0: IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) ^ Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:5463:0: IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310 ^ Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10090:0: V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA) ^ Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10008:0: IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) ^ Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10003:0: LK = DMAX1(LK, PHI*W(PHIPIN)) ^ Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10144:0: IF (KA .GE. KAMIN) GO TO 340 ^ Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11900:0: V(NREDUC) = NRED ^ Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11903:0: V(DST0) = DNWTST ^ Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2390:0: V(NREDUC) = NRED ^ Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2389:0: 60 V(DST0) = DS0 ^ Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:7892:0: V(NREDUC) = NRED ^ Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:7891:0: 90 V(DST0) = DS0 ^ Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8370:0: 210 IV(FDH) = HES ^ Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:3456:0: IF (LIV .LT. MIV2) GO TO 300 ^ Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11737:0: 270 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) ^ Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11694:0: CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1)) ^ Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11694:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:440:0: 300 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) ^ Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:348:0: CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1)) ^ Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:348:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized] x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/datasets' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/datasets' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c making init.d from init.c making methods_list_dispatch.d from methods_list_dispatch.c making slot.d from slot.c making class_support.d from class_support.c making tests.d from tests.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c do_substitute_direct.c -o do_substitute_direct.o making utils.d from utils.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c methods_list_dispatch.c -o methods_list_dispatch.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c slot.c -o slot.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c class_support.c -o class_support.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c tests.c -o tests.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c utils.c -o utils.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/methods' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid/src' making gpar.d from gpar.c making grid.d from grid.c making just.d from just.c making layout.d from layout.c making matrix.d from matrix.c making register.d from register.c making state.d from state.c making unit.d from unit.c making util.d from util.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gpar.c -o gpar.o making viewport.d from viewport.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c grid.c -o grid.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c just.c -o just.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c layout.c -o layout.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c register.c -o register.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c state.c -o state.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c unit.c -o unit.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c viewport.c -o viewport.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/grid' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines/src' making splines.d from splines.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c splines.c -o splines.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/splines' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats4' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats4' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/stats4' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o making tcltk_unix.d from tcltk_unix.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c tcltk.c -o tcltk.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c tcltk_unix.c -o tcltk_unix.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11 -lm -L../../../../lib -lR make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk/src' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk' byte-compiling package 'tcltk' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/tcltk' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o making fork.d from fork.c x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rngstream.c -o rngstream.o x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fork.c -o fork.o x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel/src' make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel/src' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' byte-compiling package 'parallel' make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/parallel' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/base' installing parsed NAMESPACE files make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' you should 'make docs' now ... make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/doc' configuring Java ... Java interpreter : /usr/lib/jvm/java/jre/bin/java Java version : 1.8.0_144 Java home path : /usr/lib/jvm/java Java compiler : /usr/lib/jvm/java/bin/javac Java headers gen.: /usr/lib/jvm/java/bin/javah Java archive tool: /usr/lib/jvm/java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm make[2]: Entering directory `/usr/src/tmp/Rjavareconf.G5pESz' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c conftest.c -o conftest.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib/jvm/java/jre/lib/amd64/server -ljvm -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[2]: Leaving directory `/usr/src/tmp/Rjavareconf.G5pESz' JAVA_HOME : /usr/lib/jvm/java Java library path: $(JAVA_HOME)/jre/lib/amd64/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm Updating Java configuration in /usr/src/RPM/BUILD/R-3.4.3 Done. make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3' creating doc/NEWS creating doc/NEWS.pdf make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-admin.html creating doc/manual/R-exts.html creating doc/manual/R-data.html creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/doc/html' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc/html' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc/manual' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' installing parsed Rd make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' grDevices grid methods tcltk tools datasets graphics splines compiler stats4 parallel utils base stats make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' building/updating package metadata ... make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' writing package indices make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' building all R object docs converting help for package 'base' Arithmetic html Rd warning: /usr/src/RPM/BUILD/R-3.4.3/src/library/base/man/Arithmetic.Rd:158: missing file link 'Ops' AsIs html Bessel html CallExternal html Colon html Comparison html Rd warning: /usr/src/RPM/BUILD/R-3.4.3/src/library/base/man/Comparison.Rd:101: missing file link 'Ops' Constants html Control html Cstack_info html DateTimeClasses html Dates html Defunct html Deprecated html Encoding html EnvVar html Extract html Extract.data.frame html Extract.factor html Extremes html Foreign-internal html Foreign html Hyperbolic html ISOdatetime html Internal html InternalMethods html La_library html La_version html Last.value html Log html Logic html Rd warning: /usr/src/RPM/BUILD/R-3.4.3/src/library/base/man/Logic.Rd:105: missing file link 'Ops' LongVectors html MathFun html Memory-limits html Memory html NA html NULL html NumericConstants html Ops.Date html Paren html Platform html Primitive html Quotes html Random-user html Random html RdUtils html Recall html Reserved html Rhome html Round html Special html Startup html Syntax html Sys.getenv html Sys.getpid html Sys.glob html Sys.info html Sys.localeconv html Sys.readlink html Sys.setFileTime html Sys.setenv html Sys.sleep html Sys.time html Sys.which html Trig html UseMethod html Vectorize html Version html abbreviate html agrep html all html all.equal html allnames html any html aperm html append html apply html args html array html as.Date html as.POSIXlt html Rd warning: /usr/src/RPM/BUILD/R-3.4.3/src/library/base/man/as.POSIXlt.Rd:126: missing file link 'format.POSIXlt' as.data.frame html as.environment html as.function html assign html assignOps html attach html attr html attributes html autoload html backsolve html base-defunct html base-deprecated html base-internal html base-package html basename html bincode html bindenv html bitwise html body html bquote html browser html browserText html builtins html by html c html call html callCC html capabilities html cat html cbind html char.expand html character html charmatch html chartr html chkDots html chol html chol2inv html class html col html colSums html colnames html commandArgs html comment html complex html conditions html conflicts html connections html contributors html copyright html crossprod html cumsum html curlGetHeaders html cut.POSIXt html cut html data.class html data.frame html data.matrix html dataframeHelpers html date html dcf html debug html Rd warning: /usr/src/RPM/BUILD/R-3.4.3/src/library/base/man/debug.Rd:73: missing file link 'isRematched' delayedAssign html deparse html deparseOpts html det html detach html dev html diag html diff html difftime html dim html dimnames html do.call html dontCheck html double html dput html drop html droplevels html dump html duplicated html dynload html eapply html eigen html encodeString html environment html eval html exists html expand.grid html expression html extSoftVersion html factor html file.access html file.choose html file.info html file.path html file.show html files html files2 html find.package html findInterval html force html forceAndCall html formals html format html format.info html format.pval html formatDL html formatc html function html funprog html gc html gc.time html gctorture html get html getCallingDLL html getDLLRegisteredRoutines html getLoadedDLLs html getNativeSymbolInfo html gettext html getwd html gl html grep html grepRaw html groupGeneric html grouping html gzcon html hexmode html iconv html icuSetCollate html identical html identity html ifelse html integer html interaction html interactive html invisible html is.finite html is.function html is.language html is.object html is.recursive html is.single html is.unsorted html isR html isS4 html isSymmetric html jitter html kappa html kronecker html l10n_info html labels html lapply html lazyload html length html lengths html levels html libPaths html libcurlVersion html library html library.dynam html license html list html list.files html list2env html load html locales html logical html lower.tri html ls html make.names html make.unique html mapply html margin.table html mat.or.vec html match html match.arg html match.call html match.fun html matmult html matrix html maxCol html mean html memCompress html memory.profile html merge html message html missing html mode html name html names html nargs html nchar html nlevels html noquote html norm html normalizePath html notyet html nrow html ns-dblcolon html ns-hooks html ns-internal html ns-load html ns-reflect html ns-topenv html numeric html numeric_version html octmode html on.exit html options html order html outer html parse html paste html path.expand html pcre_config html pmatch html polyroot html pos.to.env html pretty html print html Rd warning: /usr/src/RPM/BUILD/R-3.4.3/src/library/base/man/print.Rd:82: missing file link '.print.via.format' print.dataframe html print.default html prmatrix html proc.time html prod html prop.table html pushBack html qr html qraux html quit html range html rank html rapply html raw html rawConnection html rawConversion html readBin html readChar html readLines html readRDS html readRenviron html readline html reg.finalizer html regex html regmatches html rep html replace html rev html rle html rm html round.POSIXt html row html row.names html rowsum html sQuote html sample html save html scale html scan html search html seek html seq.Date html seq.POSIXt html seq html sequence html serialize html setTimeLimit html sets html shQuote html showConnections html sign html sink html slice.index html slotOp html socketSelect html solve html sort html source html split html sprintf html srcfile html standardGeneric html startsWith html stop html stopifnot html strptime html strrep html strsplit html strtoi html strtrim html structure html strwrap html subset html substitute html substr html sum html summary html svd html sweep html switch html sys.parent html sys.source html system html system.file html system.time html system2 html t html table html tabulate html tapply html taskCallback html taskCallbackManager html taskCallbackNames html tempfile html textconnections html tilde html timezones html toString html trace html traceback html tracemem html transform html trimws html try html typeof html unique html unlink html unlist html unname html userhooks html utf8Conversion html validUTF8 html vector html warning html warnings html weekday.POSIXt html which html which.min html with html withVisible html write html writeLines html xtfrm html zMachine html zScript html zapsmall html zpackages html zutils html Signals html converting help for package 'tools' CRANtools html HTMLheader html HTMLlinks html QC html Rcmd html Rd2HTML html Rd2txt_options html RdTextFilter html Rdiff html Rdindex html Rdutils html SweaveTeXFilter html add_datalist html assertCondition html bibstyle html buildVignette html buildVignettes html charsets html checkFF html checkMD5sums html checkPoFiles html checkRd html checkRdaFiles html checkTnF html checkVignettes html check_packages_in_dir html Rd warning: /usr/src/RPM/BUILD/R-3.4.3/src/library/tools/man/check_packages_in_dir.Rd:121: missing file link 'parLapply' codoc html compactPDF html delimMatch html dependsOnPkgs html encoded html fileutils html find_gs_cmd html getVignetteInfo html loadRdMacros html makeLazyLoading html make_translations_pkg html makevars html md5sum html package_dependencies html package_native_routine_registration_skeleton html parseLatex html parse_Rd html print.via.format html pskill html psnice html read.00Index html showNonASCII html startDynamicHelp html testInstalledPackage html texi2dvi html toHTML html toRd html toTitleCase html tools-defunct html tools-deprecated html tools-package html undoc html update_pkg_po html vignetteDepends html vignetteEngine html writePACKAGES html xgettext html converting help for package 'utils' BATCH html INSTALL html PkgUtils html Question html REMOVE html RHOME html RShowDoc html RSiteSearch html Rprof html Rprofmem html Rscript html Rtangle html RweaveLatex html SHLIB html Sweave html SweaveSyntConv html SweaveUtils html URLencode html View html adist html alarm html apropos html aregexec html aspell-utils html aspell html available.packages html bibentry html browseEnv html browseURL html browseVignettes html bug.report html capture.output html changedFiles html chooseBioCmirror html chooseCRANmirror html citEntry html citation html cite html close.socket html combn html compareVersion html contrib.url html count.fields html create.post html data html dataentry html debugcall html debugger html demo html download.file html download.packages html edit html edit.data.frame html example html file.edit html filetest html findLineNum html fix html flush.console html format html getAnywhere html getFromNamespace html getParseData html getS3method html glob2rx html globalVariables html hasName html head html help html help.request html help.search html help.start html hsearch-utils html install.packages html installed.packages html isS3method html isS3stdGen html localeToCharset html ls_str html maintainer html make.packages.html html make.socket html menu html methods html mirrorAdmin html modifyList html news html object.size html package.skeleton html packageDescription html packageName html packageStatus html page html person html process.events html prompt html promptData html promptPackage html rcompgen html read.DIF html read.fortran html read.fwf html read.socket html read.table html recover html relist html remove.packages html removeSource html roman html rtags html savehistory html select.list html sessionInfo html setRepositories html sourceutils html stack html str html strcapture html summaryRprof html tar html toLatex html txtProgressBar html type.convert html untar html unzip html update.packages html url.show html utils-defunct html utils-deprecated html utils-package html vignette html write.table html zip html COMPILE html LINK html memory.size html nsl html converting help for package 'grDevices' Devices html Hershey html Japanese html Type1Font html adjustcolor html as.graphicsAnnot html as.raster html axisTicks html boxplot.stats html cairo html check.options html chull html cm html col2rgb html colorRamp html colors html contourLines html convertColor html densCols html dev html dev.capabilities html dev.capture html dev.flush html dev.interactive html dev.size html dev2 html dev2bitmap html devAskNewPage html embedFonts html extendrange html getGraphicsEvent html grDevices-package html grSoftVersion html gray html gray.colors html hcl html hsv html make.rgb html n2mfrow html nclass html palette html palettes html pdf html pdf.options html pictex html plotmath html postscript html postscriptFonts html pretty.Date html ps.options html recordGraphics html recordplot html rgb html rgb2hsv html trans3d html xfig html xy.coords html xyTable html xyz.coords html png html quartz html quartzFonts html savePlot html x11 html x11Fonts html converting help for package 'graphics' abline html arrows html assocplot html axTicks html axis.POSIXct html axis html barplot html box html boxplot html boxplot.matrix html bxp html cdplot html clip html contour html convertXY html coplot html curve html dotchart html filled.contour html fourfoldplot html frame html graphics-defunct html graphics-package html grid html hist.POSIXt html hist html identify html image html layout html legend html lines html locator html matplot html mosaicplot html mtext html pairs html panel.smooth html par html persp html pie html plot html plot.dataframe html plot.default html plot.design html plot.factor html plot.formula html plot.raster html plot.table html plot.window html plot.xy html plothistogram html points html polygon html polypath html rasterImage html rect html rug html screen html segments html smoothScatter html spineplot html stars html stem html stripchart html strwidth html sunflowerplot html symbols html text html title html units html xspline html zAxis html converting help for package 'stats' AIC html ARMAacf html ARMAtoMA html Beta html Binomial html Cauchy html Chisquare html Distributions html Exponential html Fdist html GammaDist html Geometric html HoltWinters html Hypergeometric html IQR html KalmanLike html Logistic html Lognormal html Multinom html NLSstAsymptotic html NLSstClosestX html NLSstLfAsymptote html NLSstRtAsymptote html NegBinomial html Normal html Poisson html SSD html SSasymp html SSasympOff html SSasympOrig html SSbiexp html SSfol html SSfpl html SSgompertz html SSlogis html SSmicmen html SSweibull html SignRank html StructTS html TDist html Tukey html TukeyHSD html Uniform html Weibull html Wilcoxon html acf html acf2AR html add1 html addmargins html aggregate html alias html anova html anova.glm html anova.lm html anova.mlm html ansari.test html aov html approxfun html ar html ar.ols html arima html arima.sim html arima0 html as.hclust html asOneSidedFormula html ave html bandwidth html bartlett.test html binom.test html biplot html biplot.princomp html birthday html box.test html cancor html case.names html checkMFClasses html chisq.test html cmdscale html coef html complete.cases html confint html constrOptim html contrast html contrasts html convolve html cophenetic html cor html cor.test html cov.wt html cpgram html cutree html decompose html delete.response html dendrapply html dendrogram html density html deriv html deviance html df.residual html diffinv html dist html dummy.coef html ecdf html eff.aovlist html effects html embed html expand.model.frame html extractAIC html factanal html factor.scope html family html fft html filter html fisher.test html fitted.values html fivenum html fligner.test html formula html formula.nls html friedman.test html ftable html ftable.formula html getInitial html glm html glm.control html glm.summaries html hclust html heatmap html identify.hclust html influence.measures html integrate html interaction.plot html is.empty html isoreg html kernapply html kernel html kmeans html kruskal.test html ks.test html ksmooth html lag html lag.plot html line html listof html lm html lm.influence html lm.summaries html lmfit html loadings html loess html loess.control html logLik html loglin html lowess html ls.diag html ls.print html lsfit html mad html mahalanobis html make.link html makepredictcall html manova html mantelhaen.test html mauchly.test html mcnemar.test html median html medpolish html model.extract html model.frame html model.matrix html model.tables html monthplot html mood.test html na.action html na.contiguous html na.fail html nafns html naprint html nextn html nlm html nlminb html nls html nls.control html nobs html numericDeriv html offset html oneway.test html optim html optimize html order.dendrogram html p.adjust html pairwise.prop.test html pairwise.t.test html pairwise.table html pairwise.wilcox.test html plot.HoltWinters html plot.acf html plot.density html plot.isoreg html plot.lm html plot.ppr html plot.profile.nls html plot.spec html plot.stepfun html plot.ts html poisson.test html poly html power html power.anova.test html power.prop.test html power.t.test html pp.test html ppoints html ppr html prcomp html predict.HoltWinters html predict html predict.arima html predict.glm html predict.lm html predict.loess html predict.nls html predict.smooth.spline html preplot html princomp html print.power.htest html print.ts html printCoefmat html profile html profile.nls html proj html prop.test html prop.trend.test html qqnorm html quade.test html quantile html r2dtable html rWishart html read.ftable html rect.hclust html relevel html reorder.dendrogram html reorder.factor html replications html reshape html residuals html runmed html scatter.smooth html screeplot html sd html se.contrast html selfStart html setNames html shapiro.test html sigma html simulate html smooth html smooth.spline html smoothEnds html sortedXyData html spec.ar html spec.pgram html spec.taper html spectrum html splinefun html start html stat.anova html stats-defunct html stats-deprecated html stats-package html step html stepfun html stl html stlmethods html summary.aov html summary.glm html summary.lm html summary.manova html summary.nls html summary.princomp html supsmu html symnum html t.test html termplot html terms html terms.formula html terms.object html time html toeplitz html ts-methods html ts html ts.plot html ts.union html tsSmooth html tsdiag html tsp html uniroot html update html update.formula html var.test html varimax html vcov html weighted.mean html weighted.residuals html weights html wilcox.test html window html xtabs html zC html converting help for package 'datasets' AirPassengers html BJsales html BOD html ChickWeight html DNase html EuStockMarkets html Formaldehyde html HairEyeColor html Harman23.cor html Harman74.cor html Indometh html InsectSprays html JohnsonJohnson html LakeHuron html LifeCycleSavings html Loblolly html Nile html Orange html OrchardSprays html PlantGrowth html Puromycin html Theoph html Titanic html ToothGrowth html UCBAdmissions html UKDriverDeaths html UKLungDeaths html UKgas html USAccDeaths html USArrests html USJudgeRatings html USPersonalExpenditure html VADeaths html WWWusage html WorldPhones html ability.cov html airmiles html airquality html anscombe html attenu html attitude html austres html beavers html cars html chickwts html co2 html crimtab html datasets-package html discoveries html esoph html euro html eurodist html faithful html freeny html infert html iris html islands html lh html longley html lynx html morley html mtcars html nhtemp html nottem html npk html occupationalStatus html precip html presidents html pressure html quakes html randu html rivers html rock html sleep html stackloss html state html sunspot.month html sunspot.year html sunspots html swiss html treering html trees html uspop html volcano html warpbreaks html women html zCO2 html converting help for package 'methods' BasicClasses html Classes html Classes_Details html Documentation html EmptyMethodsList-class html EnvironmentClass html GenericFunctions html Introduction html LanguageClasses html LinearMethodsList-class html MethodDefinition-class html MethodSupport html MethodWithNext-class html Methods html MethodsList-class html MethodsList html Methods_Details html Methods_for_Nongenerics html Methods_for_S3 html NextMethod html ObjectsWithPackage-class html RClassUtils html RMethodUtils html S3Part html S4groupGeneric html SClassExtension-class html StructureClasses html TraceClasses html as html callGeneric html canCoerce html cbind2 html className html classRepresentation-class html classesToAM html dotsMethods html evalSource html findClass html findMethods html fixPrevious html genericFunction-class html getClass html getMethod html getPackageName html hasArg html implicitGeneric html inheritedSlotNames html initialize-methods html is html isSealedMethod html languageEl html localRefClass html method.skeleton html methodUtilities html methods-defunct html methods-deprecated html methods-package html new html nonStructure-class html promptClass html promptMethods html refClass html removeMethod html representation html selectSuperClasses html setAs html setClass html setClassUnion html setGeneric html setGroupGeneric html setIs html setLoadActions html setMethod html setOldClass html setSClass html show html showMethods html signature-class html slot html stdRefClass html substituteDirect html testInheritedMethods html validObject html zBasicFunsList html converting help for package 'grid' Grid html absolute.size html arrow html calcStringMetric html current.viewport html dataViewport html depth html drawDetails html editDetails html explode html gEdit html gPath html getNames html gpar html grid-defunct html grid-internal html grid-package html grid.DLapply html grid.add html grid.bezier html grid.cap html grid.circle html grid.clip html grid.convert html grid.copy html grid.curve html grid.delay html grid.display.list html grid.draw html grid.edit html grid.force html grid.frame html grid.function html grid.get html grid.grab html grid.grep html grid.grill html grid.grob html grid.layout html grid.lines html grid.locator html grid.ls html grid.move.to html grid.newpage html grid.null html grid.pack html grid.path html grid.place html grid.plot.and.legend html grid.points html grid.polygon html grid.pretty html grid.raster html grid.record html grid.rect html grid.refresh html grid.remove html grid.reorder html grid.roundrect html grid.segments html grid.set html grid.show.layout html grid.show.viewport html grid.text html grid.xaxis html grid.xspline html grid.yaxis html grobName html grobWidth html grobX html legendGrob html makeContent html plotViewport html resolveRasterSize html showGrob html showViewport html stringWidth html unit html unit.c html unit.length html unit.pmin html unit.rep html valid.just html validDetails html viewport html viewports html vpPath html widthDetails html xDetails html xsplinePoints html converting help for package 'splines' asVector html backSpline html bs html interpSpline html ns html periodicSpline html polySpline html predict.bSpline html predict.bs html splineDesign html splineKnots html splineOrder html splines-package html xyVector html converting help for package 'stats4' coef-methods html confint-methods html logLik-methods html mle-class html mle html plot-methods html profile-methods html profile.mle-class html show-methods html stats4-package html summary-methods html summary.mle-class html update-methods html vcov-methods html converting help for package 'tcltk' TclInterface html TkCommands html TkWidgetcmds html TkWidgets html tclServiceMode html tcltk-defunct html tcltk-package html tkProgressBar html tkStartGUI html tk_choose.dir html tk_choose.files html tk_messageBox html tk_select.list html tkpager html converting help for package 'compiler' compile html converting help for package 'parallel' RngStream html clusterApply html detectCores html makeCluster html parallel-package html splitIndices html children html mcaffinity html mcfork html mclapply html mcparallel html pvec html make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/src/library' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/Recommended' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/src/library/Recommended' begin installing recommended package MASS begin installing recommended package lattice begin installing recommended package codetools begin installing recommended package foreign begin installing recommended package KernSmooth begin installing recommended package rpart begin installing recommended package nnet begin installing recommended package spatial * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'codetools' finding HTML links ... done checkUsage html codetools html findGlobals html showTree html ** building package indices ** testing if installed package can be loaded * DONE (codetools) Making 'packages.html' ... done * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/RtmpMczkZm/R.INSTALL1a19654893c57/nnet/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nnet.c -o nnet.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/RtmpMczkZm/R.INSTALL1a19654893c57/nnet/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nnet' finding HTML links ... done class.ind html multinom html nnet.Hess html nnet html predict.nnet html which.is.max html ** building package indices ** testing if installed package can be loaded * DONE (nnet) Making 'packages.html' ... done * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/Rtmp4SWZwp/R.INSTALL1a2804a1ccf9a/spatial/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c krc.c -o krc.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pps.c -o pps.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/Rtmp4SWZwp/R.INSTALL1a2804a1ccf9a/spatial/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'spatial' finding HTML links ... done Kaver html Kenvl html Kfn html Psim html SSI html Strauss html anova.trls html correlogram html expcov html ppgetregion html ppinit html pplik html ppregion html predict.trls html prmat html semat html surf.gls html surf.ls html trls.influence html trmat html variogram html ** building package indices ** testing if installed package can be loaded * DONE (spatial) Making 'packages.html' ... done * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/Rtmp42nYqt/R.INSTALL1a199309306bd/KernSmooth/src' f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c blkest.f -o blkest.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cp.f -o cp.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgedi.f -o dgedi.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgefa.f -o dgefa.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgesl.f -o dgesl.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c linbin.f -o linbin.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c linbin2D.f -o linbin2D.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c locpoly.f -o locpoly.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rlbin.f -o rlbin.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sdiag.f -o sdiag.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sstdiag.f -o sstdiag.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/Rtmp42nYqt/R.INSTALL1a199309306bd/KernSmooth/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'KernSmooth' finding HTML links ... done bkde html bkde2D html bkfe html dpih html dpik html dpill html locpoly html ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) Making 'packages.html' ... done * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/RtmpSRPtoo/R.INSTALL1a06b6e5cb82f/foreign/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c R_systat.c -o R_systat.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c SASxport.c -o SASxport.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c avl.c -o avl.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dbfopen.c -o dbfopen.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c file-handle.c -o file-handle.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c minitab.c -o minitab.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pfm-read.c -o pfm-read.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sfm-read.c -o sfm-read.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c spss.c -o spss.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c stataread.c -o stataread.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/RtmpSRPtoo/R.INSTALL1a06b6e5cb82f/foreign/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'foreign' finding HTML links ... done lookup.xport html read.S html read.arff html read.dbf html read.dta html read.epiinfo html read.mtp html read.octave html read.spss html read.ssd html read.systat html read.xport html write.arff html write.dbf html write.dta html write.foreign html ** building package indices ** testing if installed package can be loaded * DONE (foreign) Making 'packages.html' ... done * installing *source* package 'rpart' ... ** package 'rpart' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/Rtmpm8Votq/R.INSTALL1a24015a2e139/rpart/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c anova.c -o anova.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c anovapred.c -o anovapred.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c branch.c -o branch.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c bsplit.c -o bsplit.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c choose_surg.c -o choose_surg.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fix_cp.c -o fix_cp.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c free_tree.c -o free_tree.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gini.c -o gini.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c graycode.c -o graycode.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c insert_split.c -o insert_split.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mysort.c -o mysort.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nodesplit.c -o nodesplit.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c partition.c -o partition.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c poisson.c -o poisson.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c print_tree.c -o print_tree.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpart.c -o rpart.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpartexp.c -o rpartexp.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpcountup.c -o rpcountup.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rundown.c -o rundown.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rundown2.c -o rundown2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c surrogate.c -o surrogate.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c usersplit.c -o usersplit.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c xpred.c -o xpred.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c xval.c -o xval.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/Rtmpm8Votq/R.INSTALL1a24015a2e139/rpart/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rpart' finding HTML links ... done car.test.frame html car90 html cu.summary html kyphosis html labels.rpart html meanvar.rpart html na.rpart html path.rpart html plot.rpart html plotcp html post.rpart html predict.rpart html print.rpart html printcp html prune.rpart html residuals.rpart html rpart-internal html rpart html rpart.control html rpart.exp html rpart.object html rsq.rpart html snip.rpart html solder html stagec html summary.rpart html text.rpart html xpred.rpart html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rpart) Making 'packages.html' ... done * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/RtmpOxo4Un/R.INSTALL1a053860e9f1/MASS/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c MASS.c -o MASS.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lqs.c -o lqs.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/RtmpOxo4Un/R.INSTALL1a053860e9f1/MASS/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MASS' finding HTML links ... done Aids2 html Animals html Boston html Cars93 html Cushings html DDT html GAGurine html Insurance html MASS-internal html Melanoma html Null html OME html Pima.tr html Rabbit html Rubber html SP500 html Sitka html Sitka89 html Skye html Traffic html UScereal html UScrime html VA html abbey html accdeaths html addterm html anorexia html anova.negbin html area html bacteria html bandwidth.nrd html bcv html beav1 html beav2 html biopsy html birthwt html boxcox html cabbages html caith html cats html cement html chem html con2tr html confint html contr.sdif html coop html corresp html cov.rob html cov.trob html cpus html crabs html deaths html denumerate html dose.p html drivers html dropterm html eagles html epil html eqscplot html farms html fgl html fitdistr html forbes html fractions html galaxies html gamma.dispersion html gamma.shape.glm html gehan html genotype html geyser html gilgais html ginv html glm.convert html glm.nb html glmmPQL html hills html hist.scott html housing html huber html hubers html immer html isoMDS html kde2d html lda html ldahist html leuk html lm.gls html lm.ridge html loglm html loglm1 html logtrans html lqs html mammals html mca html mcycle html menarche html michelson html minn38 html motors html muscle html mvrnorm html negative.binomial html newcomb html nlschools html npk html npr1 html oats html painters html pairs.lda html Rd warning: /usr/src/tmp/RtmpOxo4Un/R.INSTALL1a053860e9f1/MASS/man/pairs.lda.Rd:42: file link 'splom' in package 'lattice' does not exist and so has been treated as a topic parcoord html petrol html phones html plot.lda html plot.mca html plot.profile html polr html predict.glmmPQL html predict.lda html predict.lqs html predict.mca html predict.qda html profile.glm html qda html quine html rational html renumerate html rlm html rms.curv html rnegbin html road html rotifer html sammon html ships html shoes html shrimp html shuttle html snails html stdres html steam html stepAIC html stormer html studres html summary.loglm html summary.negbin html summary.rlm html survey html synth.tr html theta.md html topo html truehist html ucv html waders html whiteside html width.SJ html write.matrix html wtloss html ** building package indices ** testing if installed package can be loaded * DONE (MASS) Making 'packages.html' ... done begin installing recommended package cluster begin installing recommended package class * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/Rtmp6gKPVw/R.INSTALL73835a157849/class/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c class.c -o class.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/Rtmp6gKPVw/R.INSTALL73835a157849/class/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'class' finding HTML links ... done SOM html batchSOM html condense html knn html knn.cv html knn1 html lvq1 html lvq2 html lvq3 html lvqinit html lvqtest html multiedit html olvq1 html reduce.nn html somgrid html ** building package indices ** testing if installed package can be loaded * DONE (class) Making 'packages.html' ... done * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/Rtmp97Sepr/R.INSTALL1a0506e35e737/lattice/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c threeDplot.c -o threeDplot.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/Rtmp97Sepr/R.INSTALL1a0506e35e737/lattice/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lattice' finding HTML links ... done Lattice html Rows html USMortality html axis.default html banking html barchart.table html barley html cloud html draw.colorkey html draw.key html environmental html ethanol html histogram html interaction html lattice.options html latticeParseFormula html level.colors html levelplot html llines html lset html make.groups html melanoma html oneway html packet.panel.default html panel.axis html panel.barchart html panel.bwplot html panel.cloud html panel.densityplot html panel.dotplot html panel.functions html panel.histogram html panel.levelplot html panel.loess html panel.number html panel.pairs html panel.parallel html panel.qqmath html panel.qqmathline html panel.smoothScatter html panel.spline html panel.stripplot html panel.superpose html panel.violin html panel.xyplot html prepanel.default html prepanel.functions html print.trellis html qq html qqmath html rfs html shingles html simpleKey html simpleTheme html singer html splom html strip.default html tmd html trellis.device html trellis.object html trellis.par.get html update.trellis html utilities.3d html xyplot html xyplot.ts html ** building package indices ** testing if installed package can be loaded * DONE (lattice) Making 'packages.html' ... done begin installing recommended package Matrix begin installing recommended package nlme * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/RtmplxlD4v/R.INSTALL738e74440374/cluster/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c clara.c -o clara.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c daisy.f -o daisy.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dysta.f -o dysta.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c fanny.c -o fanny.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c mona.c -o mona.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pam.c -o pam.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sildist.c -o sildist.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c spannel.c -o spannel.o mona.c: In function 'clmona_': mona.c:261:10: warning: 'nelbb' may be used uninitialized in this function [-Wmaybe-uninitialized] ner[k] = nelbb; ^ mona.c:248:7: warning: 'lcc' may be used uninitialized in this function [-Wmaybe-uninitialized] int lcc, nelbb; ^ mona.c:235:6: warning: 'jtelz' may be used uninitialized in this function [-Wmaybe-uninitialized] km = ka + jtel2; ^ mona.c:218:17: warning: 'jtel' may be used uninitialized in this function [-Wmaybe-uninitialized] if(verbose) Rprintf(" for(j ..) -> jma=%d, jtel(.,z) = (%d, %d)", jma, jtel, jtelz); ^ mona.c:227:18: warning: 'jma' may be used uninitialized in this function [-Wmaybe-uninitialized] if (x[nel + jma * x_dim1] == 1) { ^ mona.c:211:8: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized] jtel = c + d; ^ mona.c:211:8: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] mona.c:212:9: warning: 'b' may be used uninitialized in this function [-Wmaybe-uninitialized] jtelz = a + b; ^ mona.c:212:9: warning: 'a' may be used uninitialized in this function [-Wmaybe-uninitialized] x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c twins.c -o twins.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/RtmplxlD4v/R.INSTALL738e74440374/cluster/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cluster' finding HTML links ... done agnes html agnes.object html agriculture html animals html bannerplot html chorSub html clara html clara.object html clusGap html clusplot.default html Rd warning: /usr/src/tmp/RtmplxlD4v/R.INSTALL738e74440374/cluster/man/clusplot.default.Rd:212: missing file link 'cov.mve' clusplot.partition html cluster-internal html coef.hclust html daisy html diana html dissimilarity.object html ellipsoidhull html Rd warning: /usr/src/tmp/RtmplxlD4v/R.INSTALL738e74440374/cluster/man/ellipsoidhull.Rd:36: missing file link 'cov.mve' Rd warning: /usr/src/tmp/RtmplxlD4v/R.INSTALL738e74440374/cluster/man/ellipsoidhull.Rd:87: missing file link 'cov.mve' fanny html fanny.object html flower html lower.to.upper.tri.inds html mona html mona.object html pam html pam.object html partition.object html plantTraits html plot.agnes html Rd warning: /usr/src/tmp/RtmplxlD4v/R.INSTALL738e74440374/cluster/man/plot.agnes.Rd:73: missing file link 'plot.dendrogram' plot.diana html plot.mona html plot.partition html pltree html pluton html predict.ellipsoid html print.agnes html print.clara html print.diana html print.dissimilarity html Rd warning: /usr/src/tmp/RtmplxlD4v/R.INSTALL738e74440374/cluster/man/print.dissimilarity.Rd:27: missing file link 'print.dist' print.fanny html print.mona html print.pam html ruspini html silhouette html sizeDiss html summary.agnes html summary.clara html summary.diana html summary.mona html summary.pam html twins.object html volume.ellipsoid html votes.repub html xclara html ** building package indices ** testing if installed package can be loaded * DONE (cluster) Making 'packages.html' ... done * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/RtmpFKpwQ9/R.INSTALLafdd43d42976/nlme/src' f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chol.f -o chol.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c corStruct.c -o corStruct.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c gnls.c -o gnls.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nlme.c -o nlme.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c nlmefit.c -o nlmefit.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pdMat.c -o pdMat.o f95 -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c rs.f -o rs.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/RtmpFKpwQ9/R.INSTALLafdd43d42976/nlme/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nlme' finding HTML links ... done ACF html ACF.gls html ACF.lme html Alfalfa html Assay html BodyWeight html Cefamandole html Coef html Covariate html Covariate.varFunc html Dialyzer html Dim html Dim.corSpatial html Dim.corStruct html Dim.pdMat html Earthquake html Extract.pdMat html Fatigue html Gasoline html Glucose html Glucose2 html Gun html IGF html Initialize html Initialize.corStruct html Initialize.glsStruct html Initialize.lmeStruct html Initialize.reStruct html Initialize.varFunc html LDEsysMat html Machines html MathAchSchool html MathAchieve html Matrix html Matrix.pdMat html Matrix.reStruct html Meat html Milk html Muscle html Names html Names.formula html Names.pdBlocked html Names.pdMat html Names.reStruct html Nitrendipene html Oats html Orthodont html Ovary html Oxboys html Oxide html PBG html Phenobarb html Pixel html Quinidine html Rail html RatPupWeight html Relaxin html Remifentanil html Soybean html Spruce html Tetracycline1 html Tetracycline2 html VarCorr html Variogram html Variogram.corExp html Variogram.corGaus html Variogram.corLin html Variogram.corRatio html Variogram.corSpatial html Variogram.corSpher html Variogram.default html Variogram.gls html Variogram.lme html Wafer html Wheat html Wheat2 html allCoef html anova.gls html anova.lme html as.matrix.corStruct html as.matrix.pdMat html as.matrix.reStruct html asOneFormula html asTable html augPred html balancedGrouped html bdf html coef.corStruct html coef.gnls html coef.lmList html coef.lme html coef.modelStruct html coef.pdMat html coef.reStruct html coef.varFunc html collapse html collapse.groupedData html compareFits html comparePred html corAR1 html corARMA html corCAR1 html corClasses html corCompSymm html corExp html corFactor html corFactor.corStruct html corGaus html corLin html corMatrix html corMatrix.corStruct html corMatrix.pdMat html corMatrix.reStruct html corNatural html corRatio html corSpatial html corSpher html corSymm html ergoStool html fdHess html fitted.glsStruct html fitted.gnlsStruct html fitted.lmList html fitted.lme html fitted.lmeStruct html fitted.nlmeStruct html fixed.effects html fixef.lmList html formula.pdBlocked html formula.pdMat html formula.reStruct html gapply html getCovariate html getCovariate.corStruct html getCovariate.data.frame html getCovariate.varFunc html getCovariateFormula html getData html getData.gls html getData.lmList html getData.lme html getGroups html getGroups.corStruct html getGroups.data.frame html getGroups.gls html getGroups.lmList html getGroups.lme html getGroups.varFunc html getGroupsFormula html getResponse html getResponseFormula html getVarCov html gls-internal html gls html glsControl html glsObject html glsStruct html gnls html gnlsControl html gnlsObject html gnlsStruct html groupedData html gsummary html intervals html intervals.gls html intervals.lmList html intervals.lme html isBalanced html isInitialized html lmList html lmList.groupedData html lme html lme.groupedData html lme.lmList html lmeControl html lmeObject html lmeStruct html logDet html logDet.corStruct html logDet.pdMat html logDet.reStruct html logLik.corStruct html logLik.glsStruct html logLik.gnls html logLik.gnlsStruct html logLik.lmList html logLik.lme html logLik.lmeStruct html logLik.reStruct html logLik.varFunc html model.matrix.reStruct html needUpdate html needUpdate.modelStruct html nlme html nlme.nlsList html nlmeControl html nlmeObject html nlmeStruct html nlsList html nlsList.selfStart html pairs.compareFits html pairs.lmList html pairs.lme html pdBlocked html pdClasses html pdCompSymm html pdConstruct html pdConstruct.pdBlocked html pdDiag html pdFactor html pdFactor.reStruct html pdIdent html pdLogChol html pdMat html pdMatrix html pdMatrix.reStruct html pdNatural html pdSymm html phenoModel html plot.ACF html plot.Variogram html plot.augPred html plot.compareFits html plot.gls html plot.intervals.lmList html plot.lmList html plot.lme html plot.nffGroupedData html plot.nfnGroupedData html plot.nmGroupedData html plot.ranef.lmList html plot.ranef.lme html pooledSD html predict.gls html predict.gnls html predict.lmList html predict.lme html predict.nlme html print.summary.pdMat html print.varFunc html qqnorm.gls html qqnorm.lme html quinModel html random.effects html ranef.lmList html ranef.lme html reStruct html recalc html recalc.corStruct html recalc.modelStruct html recalc.reStruct html recalc.varFunc html residuals.gls html residuals.glsStruct html residuals.gnlsStruct html residuals.lmList html residuals.lme html residuals.lmeStruct html residuals.nlmeStruct html simulate.lme html solve.pdMat html solve.reStruct html splitFormula html summary.corStruct html summary.gls html summary.lmList html summary.lme html summary.modelStruct html summary.nlsList html summary.pdMat html summary.varFunc html update.modelStruct html update.varFunc html varClasses html varComb html varConstPower html varExp html varFixed html varFunc html varIdent html varPower html varWeights html varWeights.glsStruct html varWeights.lmeStruct html ** building package indices ** testing if installed package can be loaded * DONE (nlme) Making 'packages.html' ... done * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c CHMfactor.c -o CHMfactor.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Csparse.c -o Csparse.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c TMatrix_as.c -o TMatrix_as.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Tsparse.c -o Tsparse.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c Mutils.c -o Mutils.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chm_common.c -o chm_common.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cs.c -o cs.o cs.c: In function 'cs_qr': cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable] csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai, ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cs_utils.c -o cs_utils.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dense.c -o dense.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgCMatrix.c -o dgCMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgTMatrix.c -o dgTMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dgeMatrix.c -o dgeMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dpoMatrix.c -o dpoMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dppMatrix.c -o dppMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dsCMatrix.c -o dsCMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dsyMatrix.c -o dsyMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dspMatrix.c -o dspMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtCMatrix.c -o dtCMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtTMatrix.c -o dtTMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtrMatrix.c -o dtrMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dtpMatrix.c -o dtpMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c factorizations.c -o factorizations.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ldense.c -o ldense.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c lgCMatrix.c -o lgCMatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c sparseQR.c -o sparseQR.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c abIndex.c -o abIndex.o make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD' ( cd Lib ; make clean ) make[5]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD/Lib' make[5]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD' make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD' ( cd Source ; make clean ) make[5]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD/Source' make[5]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD/Source' make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD' make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD' ( cd Source ; make clean ) make[5]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD/Source' make[5]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD/Source' make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD' make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/SuiteSparse_config' make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/SuiteSparse_config' make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD' ( cd Lib ; make -f "/usr/src/RPM/BUILD/R-3.4.3/etc/Makeconf" -f Makefile ) make[5]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o In file included from ../Core/cholmod_change_factor.c:116:0: ../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ In file included from ../Core/cholmod_change_factor.c:118:0: ../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o ../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic': ../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable] Int nsuper, xsize, ssize ; ^ ../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric': ../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^ ../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^ ../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ ../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ ../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric': ../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ; ^ ../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^ ../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_copy.c -o cholmod_copy.o In file included from /usr/src/RPM/BUILD/R-3.4.3/include/R.h:91:0, from Mutils.h:12, from sparseQR.h:4, from sparseQR.c:1: sparseQR.c: In function 'sparseQR_coef': /usr/src/RPM/BUILD/R-3.4.3/include/R_ext/RS.h:74:25: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized] #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) ^ sparseQR.c:171:53: note: 'x' was declared here double *ax = REAL(GET_SLOT(ans, Matrix_xSym)), *x; ^ ../Core/cholmod_copy.c: In function 'cholmod_copy': ../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^ ../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_dense.c -o cholmod_dense.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o In file included from ../Core/cholmod_dense.c:48:0: ../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_memory.c -o cholmod_memory.o In file included from ../Core/cholmod_dense.c:50:0: ../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ In file included from ../Core/cholmod_dense.c:52:0: ../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ ../Core/cholmod_dense.c: In function 'cholmod_eye': ../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, n, nz ; ^ ../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_sparse.c -o cholmod_sparse.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_transpose.c -o cholmod_transpose.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_triplet.c -o cholmod_triplet.o ../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse': ../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] Int p, pend, j, ncol, packed, nzmax, nz, xtype ; ^ In file included from ../Core/cholmod_transpose.c:124:0: ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ In file included from ../Core/cholmod_transpose.c:126:0: ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ In file included from ../Core/cholmod_transpose.c:128:0: ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ In file included from ../Core/cholmod_transpose.c:131:0: ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ In file included from ../Core/cholmod_transpose.c:133:0: ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ In file included from ../Core/cholmod_transpose.c:136:0: ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ In file included from ../Core/cholmod_triplet.c:108:0: ../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ In file included from ../Core/cholmod_triplet.c:110:0: ../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ In file included from ../Core/cholmod_triplet.c:112:0: ../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse': ../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable] Int i, j, p, k, stype, nrow, ncol, nz, ok ; ^ ../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable] Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_check.c -o cholmod_check.o ../Check/cholmod_check.c: In function 'check_common': ../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable] Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ; ^ ../Check/cholmod_check.c: In function 'check_dense': ../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ; ^ ../Check/cholmod_check.c: In function 'check_factor': ../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable] ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ; ^ ../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable] count, precise, init_print, ilast, lnz, head, tail, jprev, plast, ^ ../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable] Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_write.c -o cholmod_write.o ../Check/cholmod_write.c: In function 'cholmod_write_sparse': ../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable] Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o ../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2': ../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol, ^ ../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^ ../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o ../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p': ../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o In file included from ../Cholesky/cholmod_rowfac.c:164:0: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:166:0: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:168:0: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ In file included from ../Cholesky/cholmod_rowfac.c:172:0: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:174:0: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:176:0: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o In file included from ../Cholesky/cholmod_solve.c:66:0: ../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^ In file included from ../Cholesky/cholmod_solve.c:69:0: ../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^ ../Cholesky/cholmod_solve.c: In function 'iperm': ../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable] Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1934:48: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized] || (for_cholesky && psxend - psx != nsrow * nscol)) ^ ../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, ^ In file included from ../MatrixOps/cholmod_sdmult.c:46:0: ../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o In file included from ../MatrixOps/cholmod_sdmult.c:48:0: ../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o In file included from ../MatrixOps/cholmod_sdmult.c:50:0: ../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_updown.c -o cholmod_updown.o ../Modify/cholmod_updown.c: In function 'cholmod_updown_mask': ../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable] *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o In file included from ../Supernodal/cholmod_super_numeric.c:78:0: ../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ In file included from ../Supernodal/cholmod_super_numeric.c:80:0: ../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:28:0: ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ In file included from ../Supernodal/cholmod_super_solve.c:30:0: ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o ../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2': ../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable] Int totsize ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o In file included from ../Core/cholmod_change_factor.c:116:0: ../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ In file included from ../Core/cholmod_change_factor.c:118:0: ../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ ../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic': ../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable] Int nsuper, xsize, ssize ; ^ ../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric': ../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^ ../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^ ../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ ../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^ ../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric': ../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ; ^ ../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^ ../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o ../Core/cholmod_copy.c: In function 'cholmod_l_copy': ../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^ ../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o In file included from ../Core/cholmod_dense.c:48:0: ../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ In file included from ../Core/cholmod_dense.c:50:0: ../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ In file included from ../Core/cholmod_dense.c:52:0: ../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^ ../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^ ../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^ ../Core/cholmod_dense.c: In function 'cholmod_l_eye': ../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, n, nz ; ^ ../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o ../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse': ../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] Int p, pend, j, ncol, packed, nzmax, nz, xtype ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o In file included from ../Core/cholmod_transpose.c:124:0: ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ In file included from ../Core/cholmod_transpose.c:126:0: ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ In file included from ../Core/cholmod_transpose.c:128:0: ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ In file included from ../Core/cholmod_transpose.c:131:0: ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^ ../Check/cholmod_check.c: In function 'check_common': ../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable] Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ; ^ In file included from ../Core/cholmod_transpose.c:133:0: ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Check/cholmod_check.c: In function 'check_dense': ../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ; ^ ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ In file included from ../Core/cholmod_transpose.c:136:0: ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^ In file included from ../Core/cholmod_triplet.c:108:0: ../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^ In file included from ../Core/cholmod_triplet.c:110:0: ../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ In file included from ../Core/cholmod_triplet.c:112:0: ../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^ ../Check/cholmod_check.c: In function 'check_factor': ../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable] ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ; ^ ../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable] count, precise, init_print, ilast, lnz, head, tail, jprev, plast, ^ ../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable] Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, ^ ../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse': ../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable] Int i, j, p, k, stype, nrow, ncol, nz, ok ; ^ ../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable] Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o ../Check/cholmod_write.c: In function 'cholmod_l_write_sparse': ../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable] Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o ../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2': ../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol, ^ ../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^ ../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o ../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p': ../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o In file included from ../Cholesky/cholmod_rowfac.c:164:0: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:166:0: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:168:0: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ In file included from ../Cholesky/cholmod_rowfac.c:172:0: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:174:0: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^ In file included from ../Cholesky/cholmod_rowfac.c:176:0: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o In file included from ../Cholesky/cholmod_solve.c:66:0: ../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^ In file included from ../Cholesky/cholmod_solve.c:69:0: ../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^ ../Cholesky/cholmod_solve.c: In function 'iperm': ../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable] Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o In file included from ../MatrixOps/cholmod_sdmult.c:46:0: ../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ In file included from ../MatrixOps/cholmod_sdmult.c:48:0: ../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^ In file included from ../MatrixOps/cholmod_sdmult.c:50:0: ../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1934:48: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized] || (for_cholesky && psxend - psx != nsrow * nscol)) ^ ../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o ../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask': ../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable] *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:28:0: ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ In file included from ../Supernodal/cholmod_super_solve.c:30:0: ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ In file included from ../Supernodal/cholmod_super_numeric.c:78:0: ../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ In file included from ../Supernodal/cholmod_super_numeric.c:80:0: ../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o ../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2': ../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable] Int totsize ; ^ ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o make[5]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/CHOLMOD' make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.4.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colamd_global.c -o colamd_global.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c colamd.c -o colamd.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o make[5]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD/Source' make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/COLAMD' make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.4.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_1.c -o amd_i_1.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_1.c -o amd_l_1.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_2.c -o amd_i_2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_2.c -o amd_l_2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_order.c -o amd_i_order.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_order.c -o amd_l_order.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_control.c -o amd_i_control.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_control.c -o amd_l_control.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_info.c -o amd_i_info.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_info.c -o amd_l_info.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_global.c -o amd_i_global.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_global.c -o amd_l_global.o ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o make[5]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD/Source' make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/AMD' make[4]: Entering directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/SuiteSparse_config' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -DNTIMER -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c SuiteSparse_config.c -o SuiteSparse_config.o ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o make[4]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src/SuiteSparse_config' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.4.3/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.4.3/lib -lR make[3]: Leaving directory `/usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/src' installing to /usr/src/RPM/BUILD/R-3.4.3/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' ** help *** installing help indices converting help for package 'Matrix' finding HTML links ... done BunchKaufman-methods html CAex html CHMfactor-class html Cholesky-class html Cholesky html CsparseMatrix-class html Diagonal html Hilbert html KNex html KhatriRao html LU-class html Matrix-class html Matrix html MatrixClass html MatrixFactorization-class html RsparseMatrix-class html Schur-class html Schur html SparseM-conv html Subassign-methods html TsparseMatrix-class html USCounties html Xtrct-methods html abIndex-class html Rd warning: /usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/man/abIndex-class.Rd:80: missing file link 'Ops' abIseq html all-methods html all.equal-methods html atomicVector-class html band html bandSparse html bdiag html boolean-matprod html cBind html chol html chol2inv-methods html colSums html compMatrix-class html condest html dMatrix-class html ddenseMatrix-class html ddiMatrix-class html denseMatrix-class html dgCMatrix-class html dgRMatrix-class html dgTMatrix-class html dgeMatrix-class html diagU2N html diagonalMatrix-class html dpoMatrix-class html drop0 html dsCMatrix-class html dsRMatrix-class html dsparseMatrix-class html dsyMatrix-class html dtCMatrix-class html dtRMatrix-class-def html dtpMatrix-class html dtrMatrix-class html expand html expm html externalFormats html facmul html forceSymmetric html formatSparseM html generalMatrix-class html graph2T html image-methods html Rd warning: /usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/man/image-methods.Rd:53: missing file link 'panel.levelplot.raster' indMatrix-class html index-class html invPerm html is.na-methods html is.null.DN html isSymmetric-methods html isTriangular html kronecker-methods html ldenseMatrix-class html ldiMatrix-class html lgeMatrix-class html lsparseMatrix-classes html lsyMatrix-class html ltrMatrix-class html lu html matrix-products html Rd warning: /usr/src/tmp/RtmpSv05v4/R.INSTALLaf94ab48c84/Matrix/man/matrix-products.Rd:406: missing file link 'tcrossprod' nMatrix-class html ndenseMatrix-class html nearPD html ngeMatrix-class html nnzero html norm html nsparseMatrix-classes html nsyMatrix-class html ntrMatrix-class html number-class html pMatrix-class html printSpMatrix html qr-methods html rankMatrix html rcond html rep2abI html replValue-class html rleDiff-class html rsparsematrix html solve-methods html spMatrix html sparse.model.matrix html sparseLU-class html sparseMatrix-class html sparseMatrix html sparseQR-class html sparseVector-class html sparseVector html symmetricMatrix-class html symmpart html triangularMatrix-class html uniqTsparse html unpack html unused-classes html updown html ** building package indices Loading required package: Matrix ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) Making 'packages.html' ... done begin installing recommended package survival begin installing recommended package mgcv * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory `/usr/src/tmp/RtmpmizdTR/R.INSTALL13c82477aef22/survival/src' x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agexact.c -o agexact.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agfit4.c -o agfit4.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agfit5.c -o agfit5.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agmart.c -o agmart.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agmart2.c -o agmart2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agmart3.c -o agmart3.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agscore.c -o agscore.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agsurv3.c -o agsurv3.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agsurv4.c -o agsurv4.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c agsurv5.c -o agsurv5.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chinv2.c -o chinv2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chinv3.c -o chinv3.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cholesky2.c -o cholesky2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cholesky3.c -o cholesky3.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chsolve2.c -o chsolve2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c chsolve3.c -o chsolve3.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c concordance1.c -o concordance1.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxcount1.c -o coxcount1.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxdetail.c -o coxdetail.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxexact.c -o coxexact.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxfit5.c -o coxfit5.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxfit6.c -o coxfit6.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxmart.c -o coxmart.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxmart2.c -o coxmart2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxsafe.c -o coxsafe.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxscho.c -o coxscho.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c coxscore.c -o coxscore.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c dmatrix.c -o dmatrix.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c doloop.c -o doloop.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c finegray.c -o finegray.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pyears1.c -o pyears1.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pyears2.c -o pyears2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pyears3b.c -o pyears3b.o coxexact.c: In function 'coxexact': coxexact.c:151:17: warning: 'nrisk' may be used uninitialized in this function [-Wmaybe-uninitialized] if (maxdeath*nrisk > temp) temp = maxdeath*nrisk; ^ coxexact.c:309:22: warning: 'sstart' may be used uninitialized in this function [-Wmaybe-uninitialized] d0 = coxd0(ndeath, nrisk, score+sstart, dmem0, maxdeath); ^ x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c pystep.c -o pystep.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survConcordance.c -o survConcordance.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survdiff2.c -o survdiff2.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survfit4.c -o survfit4.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survfitci.c -o survfitci.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survpenal.c -o survpenal.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survreg6.c -o survreg6.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survreg7.c -o survreg7.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survregc1.c -o survregc1.o x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.4.3/include -DNDEBUG -I/usr/local/include -fpic -pipe -Wall -g -O2 -fno-strict-aliasing -c survregc2.c -o survregc2.o survfitci.c: In function 'survfitci': survfitci.c:124:43: warning: 'umat' may be used uninitialized in this function [-Wmaybe-uninitialized] for (i=0; i ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/cache/texmf/fonts/map/pdftex/ updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3]. [4] [5]TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi [6]Converting parsed Rd's to LaTeX [7] [8]. [9]. Chapter 3 [10] [11] [12] [13] [14]TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi [15] [16.] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28]. [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3385--3393 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 349134 bytes). Transcript written on R-FAQ.log. ..This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map }] [2] [-1] Chapter 1. [1] Chapter 2 [2.]TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi Cross reference values unknown; you must run TeX again. [3] [4]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [5] [6]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, [7This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] markup, glyphs, page headings, [8] tables, conditionals, indexing,TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, sectioning, toc, fonts, environments, [9] defuns, macros, cross references, [10 insertions, (./epsf.tex] This is `epsf.tex' v2.7.4 <14 February 2011> ) [11 localization,] markup, Chapter 3 [12] glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, formatting, and turning on texinfo input format.) macros, cross references, insertions,. (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [13 (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> )] localization,) (./version.texi Underfull \hbox (badness 7685) in paragraph at lines 1285--1289 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map] [15 formatting,]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. and turning on texinfo input format.) (./R-FAQ.aux Underfull \hbox (badness 10000) in paragraph at lines 1502--1506 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]:. pdf, [17] fonts,}] Chapter 4 [2 [18]] [-1] (Acknowledgements) markup, [19 glyphs, page headings, tables, conditionals, indexing,] sectioning, toc, environments, defuns, macros, Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . 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[6] [2] [26.] [27 Chapter 2] [7 [3]] [28] [4] [8 [29]] [9 [5 [30]]] Chapter 7 [31] [32) ](/usr/share/texmf/tex/texinfo/txi-en.tex Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6)] [10] [1 [33{/var/cache/texmf/fonts/map/pdftex/ updmap/pdftex.map] Chapter 8 [34] Chapter 9 [35] [11] [7 [36] [37] Appendix A] [38] [12} [8] (./R-FAQ.toc [39.]] Chapter 3] [13] [9 [-1]] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3344--3344 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40]. [-2 [10 [41]]]) [14 [42]] [-3] (./R-FAQ.toc) (./R-FAQ.toc [11 Chapter 4 [15] [43)]] Chapter 1 [44] [16 [12] [45]] [46] [17 [1 Appendix B] Chapter 2] [47 [2]] [48] [13] [49]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [3 [14] [18]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]:] pdf, fonts, [50] [15 markup, glyphs,] page headings, tables, conditionals, indexing, [51] sectioning, [19 toc, environments, [4 defuns, macros, cross references,] insertions,] [52 (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> )] Appendix C [16 [53]] localization, [5 [54]]. [17 [55 formatting, and turning on texinfo input format.)]] (./R-defs.texi [20 (/usr/share/texmf/tex/texinfo/txi-en.tex) [18] [6] [56]]) Chapter 5 (./version.texi) [21 [19 [1]{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map] [57] [7] [58] [20 Overfull \hbox (56.55324pt too wide) in paragraph at lines 4957--4957 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4995--4995 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [59] [8]] Chapter 6 [21}] [60 [22]]. [2]] [22 [-1] Chapter 1 [61] [9]] [62 [1]] [23 Chapter 7 [23 [63]]] Chapter 3 [64 [2 [10 [24]]]] [11] [65] [66 [25] [3]] [12 [4 [24]]] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2231--2231 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2233--2233 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [13 [27]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [67] [14] Appendix D [68]] [5] [25]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [28] pdf, fonts, [69] [15] Underfull \hbox (badness 10000) in paragraph at lines 2482--2484 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [29 markup, glyphs,] page headings, tables, [6 conditionals,] indexing, [26 sectioning, toc, [16] environments,] defuns, Overfull \hbox (39.30717pt too wide) in paragraph at lines 2605--2605 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [30 [70 macros,]] cross references, insertions, (./epsf.tex [7 [17 (Function and variable index)] [71 Chapter 8] This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] [27 (Concept index) [72]] [8 (Environment variable index)] [73] [74] ) (see the transcript file for additional information)] Chapter 4] [11 Output written on R-admin.pdf (77 pages, 469810 bytes). Transcript written on R-admin.log. ]} [33] [2] [-1] Chapter 1] [20 Chapter 2 [1 [12]] Appendix A Chapter 5. [2 [29 [21] [34]]] (Function and variable index)] Cross reference values unknown; you must run TeX again. [13. [30] (Concept index)] [31] [35 [14 [32]] ) (see the transcript file for additional information)]< Overfull \hbox (27.8098pt too wide) in paragraph at lines 1443--1443 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1444--1444 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1445--1445 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1446--1446 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16/usr/share/texmf-texlive/ fonts/type1/bluesky/cm/cmr7.pfb>]] [23<]/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb [17>]] [24 [38 [25 Output written on R-data.pdf (35 pages, 264676 bytes). Transcript written on R-data.log. ]] [5] [19 Chapter 6] [39 [26]] [6] [27 [20 [40]]] Chapter 7. [28] Chapter 2 [7 [41] [21]] [29] Chapter 3 [8 [42] [30] [22]] [23 [43]] [31] [44] [32] [9 [45]] [24] [33] [46] [10.] [25] Chapter 3 [26] [27] Chapter 4 [34 [28] [47]] [29 [11] Chapter 5 [30] Chapter 6 [31]] [32] [35 [33 [48]]] [34 [12] [35]] [36] [37 [49]] [38] [36] [39] [40 [37]] [13 [50] [41]] Chapter 7 [42 [51]] [38] Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [43 [14]] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4536--4536 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4538--4538 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4539--4539 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] [52 Chapter 8 [44]] [39] [45 [53]] Underfull \hbox (badness 10000) in paragraph at lines 3840--3845 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [46] [40 [54] [47]] [48] [55 [49]] [50] [41 Chapter 9 [51] [56 [52]] Chapter 10 [53] Chapter 11 [54]] Chapter 12 [55] [15 [56] (Function and variable index) [57] [57 (Concept index) [58] [59]] kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+3/600 --dpi 603 ecrm1095 ] [42] [58] Underfull \hbox (badness 10000) in paragraph at lines 3385--3393 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] [59] Chapter 8 [44] [60] [16] [17] Chapter 9 [61 [45]] [18]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [46 [62 [19]]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]:] pdf, fonts, Chapter 10 [47] Chapter 2 [48] markup, glyphs, [63 [49 page headings, tables,] conditionals, indexing,] ) (see the transcript file for additional information) defuns, macros, cross references, insertions, ) localization, [20 [64>]] formatting, and turning on texinfo input format.<) (./R-admin.aux/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi7.pfb>< [65/u sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb><] Chapter 4/usr/share/texmf-texli ve/fonts/type1/bluesky/cm/cmr7.pfb> [21] [66] [67] This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [68entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi Output written on R-FAQ.pdf (53 pages, 405106 bytes). Transcript written on R-FAQ.log. ] (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, [22 [69]] markup, glyphs, page headings, tables, conditionals, indexing, [70 sectioning, toc,]. environments, defuns, [71 macros, cross references, insertions,] (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [72) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)].) (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [73]}] [2] (./R-admin.toc [23] [-1 formatting, and turning on texinfo input format.)] (./R-data.aux [-2 [74]]) [-3] (./R-admin.toc) (./R-admin.toc Underfull \hbox (badness 10000) in paragraph at lines 6585--6592 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [75)] Chapter 1 [1] Chapter 2 [2] [76] Underfull \hbox (badness 10000) in paragraph at lines 6762--6768 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [77] [3] [78] [24) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [4 [79])] (./version.texi)] [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [80 [5]] Chapter 3 [81 Chapter 5 [25]].}] [2] (./R-data.toc [82] [6] [83] [-1 [7]]) [-2 [84] (./R-data.toc) (./R-data.toc]) (Acknowledgements) [26 [8] [85]] [86] Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . 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Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in parag [87 [9]raph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . 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Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [88]] [2 Chapter 4] [89] Chapter 1 [3] [27 [10 [90] [91]] [92] [93] [11 Underfull \hbox (badness 10000) in paragraph at lines 8057--8066 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [94]]] [95 ] Chapter 3 [12 [96]] [4] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8335--8336 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [97] [98] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8467--8467 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8495--8497 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [99] [13] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8626--8626 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [100] [5 [101]] [102] [103] Underfull \hbox (badness 7685) in paragraph at lines 1285--1289 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14] Chapter 5 [6] [104] [28 Chapter 2 [7 [15]]] [105 [8]] [9] [29 [106 Underfull \hbox (badness 10000) in paragraph at lines 1502--1506 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16].]] [10 [107]] [17 [11 [108]]] [109 [12]] Chapter 3 [13] Chapter 4 [18] [110] [14] [30 [111] Chapter 4 [15] [112] [113]] Overfull \hbox (30.03963pt too wide) in paragraph at lines 9771--9771 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [114 [16] Chapter 6] [19 [17]] [115]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [31]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, [18] [116] markup, glyphs, Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20 page headings, tables, conditionals, indexing, [19 [117 sectioning,] toc,] environments, defuns,] Chapter 5 macros, [21 cross references, insertions, (./epsf.tex [118 This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,]] formatting, and turning on texinfo input format.) [32 (./R-FAQ.aux] [20 [119] Chapter 6] [22] Chapter 5 [21] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10329--10329 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [120]TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi [33] [121] [34] [122 [35 Chapter 6 [22]] [23] [123]] [36 Chapter 7] [23] [124] [24 [37]]) (/usr/share/texmf/tex/texinfo/txi-en.tex) [125 [1{/var/cache/texmf/fonts/map/pdftex/ updmap/pdftex.map] [38 [126 [25 [24]] Chapter 7]] [39]}] [127 (./R-FAQ.toc] [25] [-1] [128 [-2]] Underfull \hbox (badness 10000) in paragraph at lines 11162--11164 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [129 [26]) [-3] [130.] (./R-FAQ.toc) [26 (./R-FAQ.toc] [131]] [132) Chapter 1] Chapter 8 [27] [133] [134 [27]] Chapter 8 [40 [135]] [41] [28] [1 [136]] Chapter 2 [2] Chapter 9 [28 [137] Chapter 9] [42 [138 [29]]] [43 [30 [3 [139]]] Chapter 7] [31] [140 Chapter 10] [44] [4 Overfull \hbox (22.06111pt too wide) in paragraph at lines 12183--12183 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [141]] Appendix A [32 [29]] [5] [142] Chapter 6 [143 (Function and variable index) [33]] [6 [30] Chapter 8] [34 (./R-data.vrs] [144] [45] [145] [7 Chapter 9] [35] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [146 [8]] [36] [47] [37] Appendix A [147 [9] [38]] [31 [148] [48] [39] Chapter 3 [149 [10])]] [11] (Concept index) [32] (./R-data.cps [49]) [33 [150] [12]] ) (see the transcript file for additional information) [13 [151 [41] [152 [16 [53] [54]]> Warning: unbalanced parentheses in @def...] [156 [42] Chapter 5 [157 [21]. [43 [44 [159 [22]]] [160] Underfull \hbox (badness 10000) in paragraph at lines 13895--13901 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [23 Output written on R-lang.pdf (57 pages, 291809 bytes). Transcript written on R-lang.log. ] [161] [162] [24 Chapter 8 [163]] [25] [45] Chapter 6 [26] [164] [165 [27]] [46 Chapter 7] [28 Overfull \hbox (22.06111pt too wide) in paragraph at lines 14306--14306 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [166]] Appendix B [47] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14354--14354 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [167] [29] [168] [169 [30]] [170] [31 [171]] [172] [48 Underfull \hbox (badness 10000) in paragraph at lines 14857--14864 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [173 [32]]] [174] Underfull \hbox (badness 10000) in paragraph at lines 14980--14984 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [175] (Concept index) [176] [177] kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+3/600 --dpi 603 ecrm1095 [49] [33] [50] [51] [34] [52] Appendix C [53] [35] [54] [36] [55] [37] [56.] [57] [38] [58] Overfull \hbox (56.55324pt too wide) in paragraph at lines 4957--4957 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4995--4995 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [59] [60] [61] [62] [63 [39]] [64] [65] [66] [40] [67] Appendix D [68 [41]] [69 [42]] Underfull \hbox (badness 10000) in paragraph at lines 3385--3393 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] [70] (Function and variable index) [71] (./R-admin.vrs) (Concept index) [72] (./R-admin.cps) (Environment variable index) [73] (./R-admin.ens) [74] ) (see the transcript file for additional information) Loading texinfo [version 2015-06-24.23]:entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi glyphs,< page headings,/usr/share/texmf-texli ve/fonts/type1/bluesky/cm/cmtt10.pfb tables, conditionals, (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: indexing, sectioning, pdf, toc, environments,> defuns, macros, cross references, fonts,< insertions,/usr/share/texmf-texlive/fonts/type1/blue sky/cm/cmtt12.pfb (./epsf.tex> This is `epsf.tex' v2.7.4 <14 February 2011> )< localization,/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb> formatting, and turning on texinfo input format.) (./R-lang.aux Output written on R-admin.pdf (79 pages, 555635 bytes). Transcript written on R-admin.log. markup, [46 glyphs, page headings, tables, conditionals, indexing,This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. sectioning,] toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, Chapter 10 [47entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi formatting, (/usr/share/texmf/tex/texinfo/texinfo.tex and turning on texinfo input format.) (./R-data.aux Loading texinfo [version 2015-06-24.23]: pdf,] [48 fonts,] [49] ) (see the transcript file for additional information) markup, glyphs, page headings, tables, conditionals, toc, environments,< defuns,/usr/share/texmf-texlive/fonts/type1/blues ky/cm/cmmi12.pfb macros,> cross references, insertions,< (./epsf.tex/u sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,><)/usr /share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb> (./R-defs.texi< (/usr/share/texmf/tex/texinfo/txi-en.tex) formatting,/usr/share/texmf-texl ive/fonts/type1/bluesky/cm/cmsy10.pfb and turning on texinfo input format.) (./R-defs.texi> (/usr/share/texmf/tex/texinfo/txi-en.tex ) (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map (./version.texi) Output written on R-FAQ.pdf (53 pages, 405106 bytes). Transcript written on R-FAQ.log. [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map.}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [2]}] [3 [2]] (./R-data.toc [4] [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) [5] Chapter 2 [6]}] [2 [7]] (./R-lang.toc [8] Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in parag [9] [10 [-1]raph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2 [11]] Chapter 1 [3] Chapter 3 [12]] [13] [14] Chapter 4 [15] [16 [-2] [4 Chapter 5 [17]]] [18] [19] [5] [6 [20)]] [-3 Chapter 2 [7]] (./R-lang.toc) [21] (./R-lang.toc [8] [9] [22) Chapter 1] Chapter 2 [23] [10] [1] [24] [11] Chapter 6 [25] [2] [26] [12] Chapter 3 [13]mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+3/600; nonstopmode; input ecrm1095 [27] [28] Chapter 7 [29] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3 [30]]This is METAFONT, Version 2.718281 (Web2C 7.5.7) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm1095.mf (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbase.mf [14) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm.mf [31] Chapter 8] [32]PDF/LaTeX documentation: full reference index ... (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exruwest.mf Chapter 4 [15] Ok [192] [33] <./i mages/hist.pdf> [193] [34] [194] <./images/ecdf.pdf> [195] [196] <./images/QQ.pdf> [197] [35] [198] [199] [36] [200] <./images/ ice.pdf> [37] [201] [202] [203] [38] Chapter 9 [39 [204]] [16 [205] [206] [207] [208]] [209] [210] [40 [211] [212] [4 [213] [214]] [215] [216] Chapter 10 [17] [41]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] [217] [42] [218] [219] [220] [43] [44 [221] [222]] [223]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlwest.mf [45] [46 Ok [224]] [47] [225] [226] [48] [227] [49 [228] [18] Chapter 11 [229] [50] [230]] [231]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi [51] [232] [52] (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [233] [234]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. [19 [235] [53 pdf, fonts,] [236]]entering extended mode (./fullrefman.tex [237] [238] [239] LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. 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(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map) [154] [71 (/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)] (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty] (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty) [155] <./images/fig12.pdf>) Chapter 3 [72 [156]] (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) [73 (./version.tex) [8 (/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd)] [157]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrleast.mf] [1 Ok [158]{/var/cache/texmf/fonts /map/pdftex/updmap/pdftex.map [160] Chapter 9 [28] [161] [162 [74]] [163] [164] [165] [166] [167}] [75]] [168] [1] [169] [2] [9] [170]}] [1] [2] Chapter 13 [2 (./base-pkg.tex] [76 (./R-admin.toc] Chapter 1. (/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) [171] [172] Appendix A [173 [29] [10] Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3 [174]] [-1] (Function and variable index)] [175] [30] [176 Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4 (./R-data.vrs]] [-2 [77 [11 [177]] [178]] Chapter 14mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+3/600; nonstopmode; input ecrm1095 ] [179] [78] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m /n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5]) [12 [182]] [-3 [183] [184] [79 [31 [185] [186]] [6]] (./R-admin.toc [187]) (./R-admin.toc [188]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbraces.mf] Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92]) [123] [125] [95] [127] (Concept index) [32]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expunct.mf) Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80 Chapter 1 [32] Ok [14] [15] (./R-data.cps [7] [19] Appendix A [13 [81]]]) [33 [20] [13] [18] [33] [39]] [42] [43] [82 [44] [46] [47] ) (see the transcript file for additional information) [16] [5] Chapter 2 [6] [7] [2 [8] [9] [35] Ok [25] [88 [15 Cross reference values unknown; you must run TeX again. [29]] [30] [89 [190]) [67 [70]]] [71] [90 [3] [72] Appendix C [73] Output written on R-data.pdf (37 pages, 332463 bytes). Transcript written on R-data.log. [74]] [91] [75] [76] [77] [78] [79] [17 [80]] [81] [82] [83] [12 [84] [85] [4 [92 [86]] [87]]] [88] [18 [89] Appendix D [90]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrllett.mf [93 Ok [97]] [98]] [99] [19 [100] Appendix E [101] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [102]] [94] [5 [13 [103]] [104] [105] [106]] [107] Appendix F [108] [95] [109] [110] [111] [112] [14 [113] [96] [114] [115] [116]] [117] kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+3/600 --dpi 603 ecrm1095 [6 [118]] [119] [120] [20 [121] [7 [122]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrdigit.mf Ok [48]] [49] [50] [51]] [52] [53] Chapter 4 [54] [55] [56] [57]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrligtb.mf [15 Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07599pt) Font metrics written on ecrm1095.tfm. Output written on ecrm1095.603gf (256 characters, 55528 bytes). Transcript written on ecrm1095.log. [21]] [8] Overfull \hbox (0.78088pt too wide) in paragraph at lines 857--857 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [9This is METAFONT, Version 2.718281 (Web2C 7.5.7) [18]] (/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm1095.mf (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbase.mf [22 [10]] [19] Underfull \hbox (badness 1838) in paragraph at lines 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20)] [11 (/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm.mf] [21] Chapter 3 [12 [23] [22]] [23] Underfull \hbox (badness 5862) in paragraph at lines 1378--1384 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1632--1632 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1648--1654 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of [27] Underfull \hbox (badness 1303) in paragraph at lines 1658--1661 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] [24 [13 Underfull \hbox (badness 2865) in paragraph at lines 1760--1764 []\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/ m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then Underfull \hbox (badness 10000) in paragraph at lines 1764--1766 []\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by [29]] [30]] Chapter 5 Overfull \hbox (112.38031pt too wide) in paragraph at lines 1901--1901 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31 [25]] Underfull \hbox (badness 7685) in paragraph at lines 1285--1289 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14 Overfull \hbox (19.13934pt too wide) in paragraph at lines 1936--1938 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1939--1941 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32]] [26 [33]] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccess.mf [27 Overfull \hbox (4.38043pt too wide) in paragraph at lines 2193--2193 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [35]] [15] [36] Ok) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exruwest.mf Underfull \hbox (badness 1107) in paragraph at lines 2326--2328 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [37] Underfull \hbox (badness 10000) in paragraph at lines 1502--1506 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16 [28]] [17 [29] [38 Ok [192]]] Chapter 4 [18] [30] [193] Chapter 6 [31] [194 [39] [195]] [196] [197] [198] [40 [199 [32] [19]mktexpk: /usr/src/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk: successfully generated. ]] [200] [41] ) (see the transcript file for additional information) [201]< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb [203]>] Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20 [205<]/usr /share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb [34 [206]> Chapter 5] [208]] ] [214] [216] [217] Output written on R-ints.pdf (62 pages, 353836 bytes). Transcript written on R-ints.log. [218] [219] [220] [35] [221] Chapter 6 [222] [223]) [22 (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlwest.mf] Ok [224] [225] [226] [43 [227] [228] [229] [230] [231]] [232] [233] [36 [234]] [235] [37] [236] [237] [238] [239] [240] [38 [241]] Chapter 7 [39 [242]] [23 [243] [244] [245] [246]] [247] [248] [249] [250] [251] [24 Chapter 8 [40] [252]] [41] [253] [254] [44] [255]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] Chapter 9 [130] [42 [131]] [132] [25] [133] [45 [134] [43] [135]] [136] [137] Chapter 10 [44] [138] [26] [27 [139]] [140] [141] [142] [28 [45 [143]]] [144 [46] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [145] [146]] [147] [148 [47]] [149] [29] [150] [151] [152] [30 [48]] Chapter 7 [31 [153] [154]] [49] [155] [156] [157]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [50 [47] [161]] [32 [162] [163]] (Function and Variable Index) [51] (./R-lang.vrs [164] [165] [166] [167] [33 [168] [169] [52 [170]] Chapter 8 [34] [171]] [172]) [173] (Concept Index) [53 [48] [174] (./R-lang.cps [175] Chapter 9 [35 [176]]] [177] [178] [179] [180] [181]) [36 Appendix A] [49] [54 [182] [37] Appendix A [183] [38] [184]] [55] ) (see the transcript file for additional information)< [185]/usr/share/texmf-texlive/f onts/type1/bluesky/cm/cmb10.pfb> [39]] [126] [23] [40] [41 Overfull \hbox (27.8098pt too wide) in paragraph at lines 3344--3344 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] [60] [124]]] [32]) [19] [20] [13] [42]< [43]/us r/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb [44] [46] [47] [58] [59] [61] [96] [189]> [17] [45] Ok [0] [1] [2] [3] [42 [4] [50] [5] Output written on R-lang.pdf (60 pages, 409696 bytes). Transcript written on R-lang.log. [6] [7] [8] [9] [10] [11]] [12]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [43 [159]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlig.mf Ok [25]] [26] [28] [27] [29] [44] [30] [31]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrulett.mf [51 Ok [65] [66] [67] [68] [69] [70] [71] [45 [72]] [73] [74]] [75] [76] [77] [78] [79] [80]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [81] [82] [83] [84] [46 [85]] [86] [87] Appendix B [47 [88] [89]] [90]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107 [48] [108]] [109 [52]] [110] [111] [112] [113entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi] (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [49 [114]] [115] [116] pdf, fonts, [117] [118] [119] [120] [121] [122]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49 [50] [50] [51]] [52] [53] [54] [55] [56] [57]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07599pt) Font metrics written on ecrm1095.tfm. Output written on ecrm1095.603gf (256 characters, 55528 bytes). Transcript written on ecrm1095.log. [51] markup, [52] [53 Appendix C [53]] [54 glyphs,] page headings, [54] tables, conditionals, indexing, sectioning, [55 toc,] [55 environments, defuns, macros,] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] cross references, insertions, (./epsf.tex [56 This is `epsf.tex' v2.7.4 <14 February 2011> ) [57 localization,]] [58] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3848--3848 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [59] [57 [60]] [61] formatting, and turning on texinfo input format.) [62 (./R-defs.texi] (/usr/share/texmf/tex/texinfo/txi-en.tex) [58]) (./version.texi Underfull \hbox (badness 4927) in paragraph at lines 4071--4075 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4071--4075 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [63) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map] [64] Overfull \hbox (56.55324pt too wide) in paragraph at lines 4957--4957 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4995--4995 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [59] Underfull \hbox (badness 4595) in paragraph at lines 4215--4218 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [65}] [2] (./R-data.toc] [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) [60 [66 Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in parag]]raph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] [61 Cross reference values unknown; you must run TeX again.] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Underfull \hbox (badness 1199) in paragraph at lines 4400--4406 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- [67] [4 [62]] Underfull \hbox (badness 2573) in paragraph at lines 4411--4414 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [68] [5 [63]] [6] Underfull \hbox (badness 10000) in paragraph at lines 4491--4496 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4491--4496 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4491--4496 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [69] [64 Chapter 2] [7 Overfull \hbox (9.78043pt too wide) in paragraph at lines 4570--4570 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [70]] [8] [65] [9 [71]]mktexpk: /usr/src/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk: successfully generated. [72 [66 [10]]] ) (see the transcript file for additional information) [11 [73< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb] [12>] [13< Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [74/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb]> [67] [75< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmss10.pfb> [15] [16] [77 Output written on R-exts.pdf (180 pages, 923138 bytes). Transcript written on R-exts.log. ] [17] [78] [79] [18]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, Underfull \hbox (badness 10000) in paragraph at lines 5212--5220 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [80] markup, [19 glyphs, page headings,] tables, conditionals, [81 indexing,] sectioning, toc, environments, defuns, [70 macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] [82] formatting, (Function and variable index) and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [83]) (./version.texi) [1 [84{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [71]] [20 [85] (./R-admin.vrs] [86)] (Concept index)}] [72] [2] (./R-admin.cps (./R-ints.toc [87 Chapter 5]) (Environment variable index) [-1 [73] [21]] (./R-admin.ens) [-2 Underfull \hbox (badness 1796) in paragraph at lines 5758--5766 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [88]] (./R-ints.toc) (./R-ints.toc)) Chapter 1 [74] ) (see the transcript file for additional information) [2]< [5/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb]> Output written on R-admin.pdf (79 pages, 557929 bytes). Transcript written on R-admin.log. [91 [6] Chapter 7 [23]] [7] Underfull \hbox (badness 1635) in paragraph at lines 6116--6119 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class [92 [8]] [24] [9 [25]] Underfull \hbox (badness 3009) in paragraph at lines 6120--6123 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing Underfull \hbox (badness 1102) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6151--6159 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [93 [26]] Chapter 8 [27] [10] Chapter 9 [28] [94 [11]] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6299--6299 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [95]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Appendix A [29] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6341--6343 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [96entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (Function and variable index) [12 (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [30] pdf,] fonts, (./R-data.vrs] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6483--6486 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [97] [13 markup, glyphs, page headings,] tables, [98 conditionals, indexing,] sectioning, toc, [31 environments, defuns, macros, [99 cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> )] localization, [14] Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6666--6668 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 1067) in paragraph at lines 6708--6715 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [100]] formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (Concept index) [101) [32] (./version.texi] Underfull \vbox (badness 10000) has occurred while \output is active [102)] (./R-data.cps [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map Overfull \hbox (4.38043pt too wide) in paragraph at lines 6894--6894 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [103]) [33 [104]] ) (see the transcript file for additional information)]] [-2] (./R-lang.toc) Chapter 1 [17 [109 Chapter 2]] [1 Output written on R-data.pdf (37 pages, 334318 bytes). Transcript written on R-data.log. ] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7375--7375 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [110] [2] Underfull \hbox (badness 4595) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [111] Cross reference values unknown; you must run TeX again. [112] [113] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [114] [18 [115]] Underfull \hbox (badness 8132) in paragraph at lines 7714--7718 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7714--7718 \T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , but this can be changed by set-ting Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1062) in paragraph at lines 7733--7743 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be Overfull \hbox (4.63962pt too wide) in paragraph at lines 7765--7769 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [116] Underfull \hbox (badness 7451) in paragraph at lines 7804--7814 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7804--7814 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [117 [4]] [118] [5] [119] [19 [6]] [120] [7 [20]] [121] Chapter 2 [21] Underfull \hbox (badness 10000) in paragraph at lines 8211--8223 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8211--8223 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [122 [22] [23] Chapter 3] [8] [24] [25] Chapter 3 [26] [123] [9] [27] Chapter 4 [28] [124] [10] Underfull \hbox (badness 5802) in paragraph at lines 8420--8424 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a [125 [29]] Chapter 5 [30] [11] [126] Chapter 6 [12 [31]] [127] [32 [13]] Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [128] [33 [14]] [34] [35] [129 [36] [15]] [37] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8728--8728 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8730--8730 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [130] [38] [16 [131] [39]] [17 [40]] Underfull \hbox (badness 4254) in paragraph at lines 8891--8895 []\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so urce \T1/ptm/m/n/10 at-tribute), use [132 [18]] [41 [19]] Chapter 7 [42] Underfull \hbox (badness 1132) in paragraph at lines 8951--8958 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [133] Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [43] [20mktexpk: /usr/src/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk already exists. ] Chapter 8 Underfull \hbox (badness 1603) in paragraph at lines 9064--9067 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [134 [44] Chapter 4] [135 [21]] [136]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [45] [137] Underfull \hbox (badness 10000) in paragraph at lines 3840--3845 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [46]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi [138 (/usr/share/texmf/tex/texinfo/texinfo.tex] Loading texinfo [version 2015-06-24.23]: pdf, [47 fonts,] [48 [22 [139]]] markup, glyphs, page headings, tables, conditionals, indexing, sectioning, [23 toc, environments,] defuns, [140 macros, cross references, [49 insertions,] (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] [141] [24] Chapter 5 [142 [25] formatting, and turning on texinfo input format. [50)] (./R-admin.aux] Chapter 9 [51] [26] [52] Underfull \hbox (badness 1917) in paragraph at lines 9664--9669 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [143 Chapter 10 [53 [27]] Chapter 11 [54] Chapter 12] [55] [28 [56]] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9719--9719 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9720--9720 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [144 ) (see the transcript file for additional information) ]]< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx7.pfbThis is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. > [58]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi Chapter 6 (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]:< [31/usr/share/texmf- texlive/fonts/type1/bluesky/cm/cmmi9.pfb>]< pdf,/usr/share/texmf-texlive/fonts/type1/ bluesky/cm/cmr10.pfb fonts,) (Concept index)> [59 < (./R-ints.cps/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb> [146]) markup,] ) (see the transcript file for additional information) sectioning, toc,This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. environments,< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb] defuns,>>> [34 This is `epsf.tex' v2.7.4 <14 February 2011> )<> localization,]/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy9.pfb >>>< and turning on texinfo input format./usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb) [148)>> [36> Output written on R-ints.pdf (64 pages, 438199 bytes). Transcript written on R-ints.log. ))] (./version.texi) [149] Output written on R-intro.pdf (99 pages, 531351 bytes). Transcript written on R-intro.log. (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map markup, [37 glyphs,] page headings, tables, conditionals, indexing, sectioning, toc, environments, [150 defuns, [38 macros,] cross references,}] Chapter 7] [39 [2]] (./R-admin.toc insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [-1}] [2] (./R-exts.toc] [-1 Overfull \hbox (9.78043pt too wide) in paragraph at lines 10201--10201 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [151]] [-2 Chapter 8 formatting, and turning on texinfo input format.)] [40 (./R-data.aux [-2] [41] Underfull \hbox (badness 1629) in paragraph at lines 10275--10279 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [152]] Chapter 9) [-3 [42 [-3]]] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [153) (./R-admin.toc [-4]) (./R-admin.toc [43]] (./R-exts.toc) (./R-exts.toc) Chapter 10 Chapter 1 [44]) (Acknowledgements) Underfull \hbox (badness 3690) in paragraph at lines 10389--10397 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10398--10400 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than Underfull \hbox (badness 3735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [154] Chapter 1 [1] Cross reference values unknown; you must run TeX again. [45 [155]] [2] [156 [3]] [4 Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46 [1]] [5] [47 Underfull \hbox (badness 10000) in paragraph at lines 10624--10627 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [157] Chapter 2] [2]] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [158 [7])] (./version.texi) [1 [8{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map] [48 [159 [9]]] [3] [10] [4 [49] [160 [11]]] [5 [12]]} [6]] [2 [161] [7] (./R-data.toc] [13 [50]] [8] [14] [162 [-1 [9]] (Function and Variable Index)] [51)] [-2] [15 (./R-data.toc) [10 (./R-data.toc]) (./R-lang.vrs (Acknowledgements)] [11 [16 [163]] Chapter 3] [12] [17] [18] [52 [19] Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . 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Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . 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Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in parag [13 [164] [20]]) (Concept Index) Underfull \hbox (badness 7685) in paragraph at lines 1285--1289 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14 [53]] [21]] (./R-lang.cps [22] [23]raph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . 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Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [24 [2]] Chapter 1 [3 [25 [165]]] [15] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2231--2231 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2233--2233 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [27] [28]) Underfull \hbox (badness 10000) in paragraph at lines 1502--1506 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16 Underfull \hbox (badness 10000) in paragraph at lines 2482--2484 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [29 Appendix A]] [54 [17 Overfull \hbox (39.30717pt too wide) in paragraph at lines 2605--2605 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [30]]] Chapter 4 [18 [31] [55]] ) (see the transcript file for additional information) Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20]] [36 Output written on R-lang.pdf (60 pages, 413876 bytes). Transcript written on R-lang.log. ] [37 [4] [23] [38]] [39 Underfull \hbox (badness 10000) in paragraph at lines 11376--11378 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [167] [24] [40]] [25 [41]] [42] [5] [43] [44 [168]] [6 [26] [45 Underfull \hbox (badness 4569) in paragraph at lines 11493--11497 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11493--11497 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [169]]] [170] Chapter 2 [7 Underfull \hbox (badness 10000) in paragraph at lines 11608--11610 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as Underfull \hbox (badness 2790) in paragraph at lines 11651--11653 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [171]] [27] [46] [172 [8]] [9 [47 [28]]] [173 [48]] [49] Underfull \hbox (badness 4048) in paragraph at lines 11822--11832 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 11822--11832 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [174] [50] [10] [51 [29] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4536--4536 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4538--4538 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4539--4539 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] [52 [175]] [11] [53]] [54 [176]] [55] [12] [56 Chapter 3] [13] [57 Underfull \hbox (badness 5460) in paragraph at lines 12070--12079 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [177]] [30 [58]] Chapter 7 [178 [59 [31]]] [60] [179] [61] [14] [62] [180 Chapter 4] [15 Chapter 2 [63]] [32] [181 [64]] [65] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12444--12444 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [182] [66 [16]] [33 [67]] [17 Chapter 8 [34] [68]] [183]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Chapter 9 [69 [35]] [70]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi [36 (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf,] fonts, [184entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi [71 (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]:] pdf,] fonts, [37 markup,] Appendix A glyphs, page headings, [38] tables, [72 conditionals, [185 indexing,] markup, sectioning,] toc, glyphs, [18 page headings, tables, conditionals, environments, defuns,] macros, cross references, insertions, (./epsf.tex indexing, sectioning, This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [73 Underfull \hbox (badness 5119) in paragraph at lines 12729--12732 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [186] toc, environments,] [39 defuns, [74 [19] macros, cross references, formatting, and turning on texinfo input format.]) (./R-ints.aux insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) [187 Underfull \hbox (badness 10000) in paragraph at lines 6585--6592 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [75]]] localization, [76] Underfull \hbox (badness 2221) in paragraph at lines 12889--12898 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s [188] Underfull \hbox (badness 10000) in paragraph at lines 6762--6768 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [77] [20] [78] [189 Chapter 5 formatting, and turning on texinfo input format.)] [21] (./R-defs.texi [79 Overfull \hbox (27.8098pt too wide) in paragraph at lines 3344--3344 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] (/usr/share/texmf/tex/texinfo/txi-en.tex) [190] [80])] Chapter 3 (./version.texi [81]) [191 [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [82]] [83] Chapter 6 [84] [41) Underfull \hbox (badness 2253) in paragraph at lines 13141--13143 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [192 [22 (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)]]) (./version.texi)] [85 [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map] [86] [87] [193] [88] Chapter 7 Chapter 4 [89] [23]}This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] [90] [2] (./R-ints.toc [91 Underfull \hbox (badness 10000) in paragraph at lines 13256--13258 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with [194]] [92 [-1]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]:] [93}] pdf, [195 [42)] [-2 Underfull \hbox (badness 10000) in paragraph at lines 8057--8066 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [94]] fonts, [2]] (./R-ints.toc)] (./R-ints.toc (./R-intro.toc) Chapter 1 [95 [43] [24] markup, [1] [-1 [96 Underfull \hbox (badness 10000) in paragraph at lines 13406--13408 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [196 glyphs, page headings,]] tables, conditionals, [44 indexing,] sectioning,]] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8335--8336 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [97 toc, [25] environments, defuns,] [197 macros, cross references,] insertions, (./epsf.tex [98 [45 This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [2]] [-2]] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8467--8467 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8495--8497 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [99 [46]] Underfull \hbox (badness 10000) in paragraph at lines 13514--13518 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13525--13528 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . [198] Appendix B [47 [26] [3 formatting, and turning on texinfo input format.]) (./R-lang.aux ] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8626--8626 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [100 [4] [-3 Overfull \hbox (30.78088pt too wide) in paragraph at lines 13566--13566 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [199] [48] [101]]] Chapter 8 [27) [102 [5]] [-4]] (./R-intro.toc [103]) (./R-intro.toc Chapter 5 [104 [49]] Chapter 9 Underfull \hbox (badness 10000) in paragraph at lines 13658--13661 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13668--13668 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [200]) [6 (Preface) [28]] Cross reference values unknown; you must run TeX again. Chapter 1 [105 [1 [50 [7]]] [106]] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13756--13756 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, [201 [8]] [107 [51] [9]] [108] Underfull \hbox (badness 7238) in paragraph at lines 13780--13787 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13780--13787 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 13780--13787 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- Underfull \hbox (badness 3965) in paragraph at lines 13788--13792 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [202] [2 [10 [52 [109]]]] Appendix A [29 Appendix C [53]] [203 [110] [11]] (Function and variable index) [54 [111 [3] [30]]] [12 [112 (./R-data.vrs] [55]] [113] [13 Overfull \hbox (30.03963pt too wide) in paragraph at lines 9771--9771 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [114]] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13951--13951 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 13952--13952 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [204 [4 [56]] [14]] [115] [31 [205 [57 [15] [116]]]] [117 [5] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1443--1443 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1444--1444 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1445--1445 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1446--1446 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16)] [58]] Chapter 2 [118 Underfull \hbox (badness 10000) in paragraph at lines 14031--14035 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14031--14035 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [206 [6] (Concept index) [32 [17]]]] (./R-data.cps Overfull \hbox (56.55324pt too wide) in paragraph at lines 4957--4957 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4995--4995 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [59] [18 [119]]) [33 [207 Overfull \hbox (16.31242pt too wide) in paragraph at lines 10329--10329 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [120]]] [60 ) (see the transcript file for additional information) [19] [7 Overfull \hbox (63.78036pt too wide) in paragraph at lines 14179--14179 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14182--14182 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [208]]] Underfull \hbox (badness 1168) in paragraph at lines 14266--14270 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14266--14270 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [209]< [126 Underfull \hbox (badness 6944) in paragraph at lines 14361--14364 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [210/usr/share/texmf-texlive/fonts/type1/bluesky /cm/cmsy10.pfb]> [63] [9 Chapter 3< [128 [64]]/usr/share/texmf-texlive/fonts/type1/blue sky/cm/cmtt9.pfb> Overfull \hbox (4.38043pt too wide) in paragraph at lines 14386--14386 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [211] Underfull \hbox (badness 10000) in paragraph at lines 11162--11164 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [129 Output written on R-data.pdf (37 pages, 332463 bytes). Transcript written on R-data.log. ] [65] [130 [27] [10]] [131 [66]] [212] Chapter 4 [132 [28]] Underfull \hbox (badness 10000) in paragraph at lines 14520--14522 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14539--14539 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14541--14541 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14544--14544 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14550--14553 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 4254) in paragraph at lines 14566--14574 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14581--14585 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [213 [133]] [67 [134]] Appendix D [68] [11 [135 [29]]] Underfull \hbox (badness 10000) in paragraph at lines 14650--14652 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so [214 Chapter 3 [136 [12] [69 [137]]]] Chapter 5 [30 [138]] Underfull \hbox (badness 10000) in paragraph at lines 14656--14660 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, Underfull \hbox (badness 10000) in paragraph at lines 14656--14660 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14661--14669 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or Underfull \hbox (badness 3601) in paragraph at lines 14695--14699 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 14695--14699 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [215]) Chapter 6 [31 (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex Overfull \hbox (4.38043pt too wide) in paragraph at lines 14762--14762 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [216)]] [70 [139] [13)] (Function and variable index) [71]] (./version.texi (./R-admin.vrs [140) (Concept index)] Overfull \hbox (25.98041pt too wide) in paragraph at lines 14784--14784 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [217 [72]]) (./R-admin.cps Overfull \hbox (22.06111pt too wide) in paragraph at lines 12183--12183 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [141 [32) (Environment variable index)] [73] [1] [218 (./R-admin.ens]{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [142 [14)] [74 Chapter 6] [219 [143]]] Chapter 4 [15] ) (see the transcript file for additional information) [220 [33] [144]] [221]]] [36]]}]] Output written on R-admin.pdf (79 pages, 555635 bytes). Transcript written on R-admin.log. [225] [148 [2]] (./R-lang.toc [149 [37] [226]] [-1 [227]] [18] [150 [228]] [19 [-2 [38] [151]]] [229] [39 Underfull \hbox (badness 2418) in paragraph at lines 15705--15709 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 15712--15715 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 15740--15747 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [230) [-3] [20] [152]] (./R-lang.toc)] [231 [153] (./R-lang.toc] [154]) [232] Chapter 1 [40 [21] [233]] [41 [155 Overfull \hbox (0.78088pt too wide) in paragraph at lines 15986--15986 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16011--16018 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [234]]] Chapter 7 [42] Warning: unbalanced parentheses in @def... Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [43 [156 [235]] Chapter 2] [1 Chapter 8 [44]] [157] [236] [22 [45 [158]] [2 [237]]] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16279--16279 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16308--16308 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [238] [159] Underfull \hbox (badness 10000) in paragraph at lines 3840--3845 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [46] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16359--16359 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16365--16369 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16365--16369 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [239 [160]] Underfull \hbox (badness 10000) in paragraph at lines 13895--13901 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [161] [47] [162 [23 [240]]] Chapter 8 [163] [48] [164] [241 [165 [49]]] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14306--14306 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [166 Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3 [24]]] Chapter 6 [25 Overfull \hbox (33.55849pt too wide) in paragraph at lines 14354--14354 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [167 [50]] [242] Chapter 9] [51] [243] [168] [52 [26]] Chapter 10 [53] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16718--16718 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [244] Chapter 11 [54] [169] Chapter 12 [55] [245] [4 [56]] [27 [170 (Function and variable index) [57 [246]]] (./R-ints.vrs] [28 [171]] [172] [58 Underfull \hbox (badness 10000) in paragraph at lines 14857--14864 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [173] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16968--16968 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [247 Chapter 7 [29]] [174] [5)] Underfull \hbox (badness 10000) in paragraph at lines 14980--14984 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [175]] (./R-exts.vrs (Concept index) [59 [30 [248]]] (./R-ints.cps [176 [249])] [60 [6 [31]] [250 [177]] ) (see the transcript file for additional information) <]/usr/share/texmf-texlive/fonts/type1/blu esky/cm/cmb10.pfb> Underfull \hbox (badness 2435) in paragraph at lines 17229--17231 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [251< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb> ]]] Underfull \hbox (badness 1867) in paragraph at lines 17271--17278 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17271--17278 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17271--17278 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17286--17288 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17294--17294 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17304--17304 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [252 (./R-exts.cps] [34]>)>] <./images/QQ.pdf [35]>>< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb>> >>> [9 Overfull \hbox (25.98041pt too wide) in paragraph at lines 17458--17458 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17464--17464 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17467--17467 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17473--17473 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [255] [39] [256] Output written on R-exts.pdf (186 pages, 1108485 bytes). 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[257] [11] [258 [40] [12]] Chapter 10 [41] [259] [42] [13 Underfull \hbox (badness 10000) in paragraph at lines 17812--17814 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [260]] [43] [14] [44] Underfull \hbox (badness 4217) in paragraph at lines 17896--17905 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 17911--17927 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [261] [45] [262 [46]] [47] [15 [48]] [49] Chapter 11 [50] [263] [51 [264]] [52] [265] [53] [16] [266] [17] Underfull \hbox (badness 4699) in paragraph at lines 18325--18328 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [267 [54]] [18] [268] [19] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18448--18448 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [269 [55]] [20 [270]] [56] Chapter 4 [57] Underfull \hbox (badness 4739) in paragraph at lines 18583--18585 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [271 [58 [21]]] [59] [60] [272] [61 [273]] Chapter 12 [62] [274] [63] [275] [64] [65] [276] [66] [67 [277]] [68 Underfull \hbox (badness 1430) in paragraph at lines 18996--19001 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 18996--19001 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [278] [22]] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19057--19062 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [279] <./image s/fig11.pdf> [71] <./images/fig12.pdf> [72] [73 [23]] Underfull \hbox (badness 10000) in paragraph at lines 19117--19124 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19117--19124 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19117--19124 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19117--19124 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19133--19135 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [280] [74] Underfull \hbox (badness 1975) in paragraph at lines 19205--19208 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [281] [75] [24 [282] Chapter 13] [76] [283] Chapter 5 [25 [284]] [285 [77]] Chapter 14 [78 [286]] [26 Underfull \hbox (badness 1077) in paragraph at lines 19600--19605 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [287]] [79] [27 Underfull \hbox (badness 10000) in paragraph at lines 19614--19621 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [288 Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80]]] Appendix A [81] Underfull \hbox (badness 10000) in paragraph at lines 19688--19692 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [289] Underfull \hbox (badness 10000) in paragraph at lines 19818--19822 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 19818--19822 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self [290] [82] [291] [83] Underfull \hbox (badness 10000) in paragraph at lines 19916--19923 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [292] Appendix B [28 [84] [293]]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [85 Underfull \hbox (badness 10000) in paragraph at lines 20037--20041 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [294]] Underfull \hbox (badness 5161) in paragraph at lines 20092--20097 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [295] [29 [86] [296]] [87entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi] (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: Overfull \hbox (6.78088pt too wide) in paragraph at lines 20259--20259 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20263--20263 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [297] pdf, [88] fonts, Underfull \hbox (badness 3343) in paragraph at lines 20319--20323 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [298] [30] [89 Overfull \hbox (4.38043pt too wide) in paragraph at lines 20405--20405 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20416--20416 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [299]] Chapter 6 [31 markup,] [300 [90] glyphs,] Appendix C page headings, [91 Overfull \hbox (9.78043pt too wide) in paragraph at lines 20525--20525 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (85.38034pt too wide) in paragraph at lines 20528--20528 []\T1/pcr/m/n/9 attach("all.RData") # safer and will warn about masked objects w/ same name in .GlobalEnv[] [301 tables,]] conditionals, indexing, sectioning, [32 Underfull \hbox (badness 6380) in paragraph at lines 20572--20577 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20630--20637 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20630--20637 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20630--20637 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [302 toc, environments,] defuns, macros,] [92] Underfull \hbox (badness 2564) in paragraph at lines 20650--20653 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 20680--20680 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [303] cross references, insertions, (./epsf.tex Appendix D [93 This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] (./R-intro.vrs Underfull \hbox (badness 1205) in paragraph at lines 20703--20708 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [304] [33] formatting, [305] and turning on texinfo input format.) (./R-admin.aux [94 [306] [34]] [307] Underfull \hbox (badness 2469) in paragraph at lines 21013--21019 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 1939) in paragraph at lines 21013--21019 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing names. Underfull \hbox (badness 10000) in paragraph at lines 21013--21019 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [308] [35] [95 [309]] [36] [310]) [37 Appendix E [96]] (./R-intro.cps [311] [38] Chapter 7 [39] [97 Underfull \hbox (badness 10000) in paragraph at lines 21327--21329 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [312]]) Appendix F [98] [99] ) (see the transcript file for additional information) ] [41] [314]< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx7.pfb Chapter 9> [42]] [44 [316] Overfull \hbox (52.98038pt too wide) in paragraph at lines 21631--21631 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 21632--21632 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21635--21635 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [317< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl9.pfb>] [318 [47 [48] [320This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] Output written on R-intro.pdf (105 pages, 679001 bytes). Transcript written on R-intro.log. [49] [321]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [50 pdf, fonts,] (Function and Variable Index) [51] (./R-lang.vrs [322)] (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [52 [1]) (Concept Index) Underfull \hbox (badness 2277) in paragraph at lines 22008--22011 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [323 [53{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map]] (./R-lang.cps markup, glyphs, page headings,) tables, conditionals, indexing, Appendix A [54 sectioning, [324 toc, environments,]] defuns, [55]} ) (see the transcript file for additional information) [2< insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb> [325] (./R-exts.aux (./R-admin.toc (./R-admin.toc Output written on R-lang.pdf (60 pages, 409696 bytes). Transcript written on R-lang.log. [1] [327 Chapter 2 [2]] [3 [328]] [4 [329]] [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 22491--22497 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22491--22497 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins [330] [8] Underfull \hbox (badness 1484) in paragraph at lines 22523--22531 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 2951) in paragraph at lines 22523--22531 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22523--22531 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [331] [9] [10 Overfull \hbox (0.78088pt too wide) in paragraph at lines 22600--22600 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [332]] [11] Underfull \hbox (badness 10000) in paragraph at lines 22651--22655 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 22651--22655 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [333] Chapter 3 [12] [334] [13] [335] Underfull \hbox (badness 7685) in paragraph at lines 1285--1289 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14] [336] [15] [337] Underfull \hbox (badness 10000) in paragraph at lines 1502--1506 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16] [338] [17] Chapter 4 [18] Underfull \hbox (badness 10000) in paragraph at lines 23091--23099 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; [339]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) Underfull \hbox (badness 3849) in paragraph at lines 23205--23210 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [340]) (./version.texi) [19 [1]{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map Underfull \hbox (badness 7308) in paragraph at lines 23282--23288 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5077) in paragraph at lines 23282--23288 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23292--23295 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23292--23295 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [341] Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20 [342] Chapter 5 [21]] Chapter 6 [22]} [343]] [23 [2]] (./R-exts.toc [24] Underfull \hbox (badness 10000) in paragraph at lines 23444--23446 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [344] [-1 [25]] [345] [-2] [26] [-3 [27]]) [-4 [28 [346]] (./R-exts.toc) (./R-exts.toc]) (Acknowledgements) Chapter 1 [1] [29] [2 [30]] Chapter 7 [31] [347 [32]] [3] [348 [33 [4]]] Chapter 8 [34] [5 [349]] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] Chapter 9 [35] [7] [36] [350 [8]] [9 [37]] Appendix A [38] [10] [351] [11] [39] [352] [12] [353] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3344--3344 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] [13This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Underfull \hbox (badness 2197) in paragraph at lines 24122--24126 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24122--24126 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24136--24140 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24136--24140 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to [354]] [41]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [14 pdf,] fonts, Underfull \hbox (badness 10000) in paragraph at lines 24229--24235 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 24229--24235 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 24242--24244 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [355] [42 markup, glyphs, [15] page headings,] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24293--24293 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [356 tables, conditionals,] indexing, sectioning, [16 toc, environments,] defuns, macros, cross references, insertions, (./epsf.tex [17 This is `epsf.tex' v2.7.4 <14 February 2011> )] localization, [357 [43 [18]]] [19] [358 [20] formatting,] and turning on texinfo input format.) (./R-intro.aux [44] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [359] [23] [24] [45] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2231--2231 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2233--2233 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [25 Underfull \hbox (badness 4120) in paragraph at lines 24572--24579 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [360]] [26] [46 [27]] [361] Underfull \hbox (badness 10000) in paragraph at lines 2482--2484 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [28] Appendix B [47 [29]] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2605--2605 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [30] Underfull \hbox (badness 1694) in paragraph at lines 24708--24711 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [362 [48 [31This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ]]] [32] [363entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi] (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [33] pdf, fonts, [49 [34]] [364] markup, [35] glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, [365 [36] defuns, macros,] cross references, insertions, [50 (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] [37] [38 Underfull \hbox (badness 1603) in paragraph at lines 24947--24949 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [366]] [39] [51] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25065--25073 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [367 formatting, and turning on texinfo input format.) (./R-lang.aux ] [40] [41 [52]] Appendix C [53 [368] [42]] [43] [54] [44] Underfull \hbox (badness 5475) in paragraph at lines 25202--25212 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25244--25247 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25259--25261 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [369 [45] [55]] [46] [56] [47] [370] [57] [48] [371] [49] [58] [50] Overfull \hbox (56.55324pt too wide) in paragraph at lines 4957--4957 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4995--4995 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [59 Overfull \hbox (32.24495pt too wide) in paragraph at lines 4536--4536 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4538--4538 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4539--4539 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] [51]] Underfull \hbox (badness 3138) in paragraph at lines 25518--25524 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25518--25524 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 25518--25524 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 25531--25534 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 25555--25557 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25567--25571 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25567--25571 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is [372] [52] [60] [53 Underfull \hbox (badness 10000) in paragraph at lines 25572--25578 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 25587--25592 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 25593--25604 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 25605--25608 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25615--25627 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 25615--25627 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a Underfull \hbox (badness 10000) in paragraph at lines 25629--25636 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25629--25636 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25629--25636 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 25629--25636 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [373]] [61)] [54 (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)] [374]) [55 (./version.texi) [62 [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map] [375]] [56 [63]] [376] [57] [64 [377]] [58}] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25963--25963 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 25976--25980 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25976--25980 \T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.y)] [378 [2] [65]]] (./R-intro.toc [59] [379 [-1] [66]] [60 [380]] [-2] [67 [381] Appendix D] [68] [61] [-3)] (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [382] [69) [-4]] (./R-intro.toc) (./version.texi) [62) (./R-intro.toc] [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map Underfull \hbox (badness 4341) in paragraph at lines 26299--26301 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26335--26341 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*, collapse=", ")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with [383) (Preface)] Chapter 2 [63] Chapter 1 [1 Overfull \hbox (42.18039pt too wide) in paragraph at lines 26357--26357 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26369--26369 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [384]] [70}]] [2] (./R-lang.toc [64 [385 (Function and variable index) [71]]] (./R-admin.vrs) [2 (Concept index) [65] [72]] [-1 (./R-admin.cps [386 [66]]]) (Environment variable index) [73 [67 [3]]] (./R-admin.ens [-2 [387 [68]]] [69) [-3]] [388 (./R-lang.toc) (./R-lang.toc)] [70]) [4 [74 Chapter 1 [389] [71] Chapter 2 [1]] [390]] ) (see the transcript file for additional information)< [72 [2]]/usr/share/texmf-texlive/f onts/type1/bluesky/cm/cmb10.pfb Underfull \hbox (badness 10000) in paragraph at lines 26802--26806 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [391>] [73] [393 [5<]/usr/share/texmf-texlive/fonts/type1/blues ky/cm/cmmi9.pfb [394>] Chapter 2 Underfull \hbox (badness 10000) in paragraph at lines 6585--6592 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [75 [4]] [397 Underfull \hbox (badness 10000) in paragraph at lines 6762--6768 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [77] [401] [84 [11]<]]/usr/share/texmf-texli ve/fonts/type1/bluesky/cm/cmtt10.pfb [402 [13] [86]>] [87] [14] [88] [90 Underfull \hbox (badness 1226) in paragraph at lines 27692--27697 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [404]] [8 [16 Output written on R-admin.pdf (79 pages, 555640 bytes). Transcript written on R-admin.log. ] [91]] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27737--27737 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [405 [17 [92]]] [93] [406] [18 Underfull \hbox (badness 10000) in paragraph at lines 8057--8066 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [94]] [19 [407 [95 [9]]]] [96 [408]] [20 [10 Overfull \hbox (15.18042pt too wide) in paragraph at lines 28003--28003 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28014--28014 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28020--28020 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28021--28021 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28024--28024 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [409]]] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8335--8336 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [97 Chapter 4 [21]] Underfull \hbox (badness 7415) in paragraph at lines 28099--28103 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [410] [98 [22]] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28120--28120 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [411 Overfull \hbox (56.55324pt too wide) in paragraph at lines 8467--8467 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8495--8497 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [99] [11]] Chapter 3 [23 [12]] Underfull \hbox (badness 2418) in paragraph at lines 28268--28279 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [412 Overfull \hbox (50.80455pt too wide) in paragraph at lines 8626--8626 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [100]] [24 [101]] Chapter 5 [102 [25]] [413] [103] Chapter 5 [13 [26 [104]]] [27 Underfull \hbox (badness 1248) in paragraph at lines 28392--28399 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 28392--28399 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [414]] [28] Underfull \hbox (badness 1533) in paragraph at lines 28501--28504 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [415 [105 [29]]] [416 [14 [106]]] [30 Chapter 4 [15]] [107 Chapter 6] [31] Underfull \hbox (badness 1337) in paragraph at lines 28598--28601 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [417] [108] [32] [16] Overfull \hbox (42.78088pt too wide) in paragraph at lines 28646--28646 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 28663--28674 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in Underfull \hbox (badness 10000) in paragraph at lines 28675--28678 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [418 [109]] [33] [419] Chapter 5 [17 [34 Underfull \hbox (badness 1117) in paragraph at lines 28770--28776 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [420 [110]]]] [18] [35 [421] [111] [19]] [422 [20]] [112 [36]] [423] [424 [37 [21 [113]]]] Overfull \hbox (30.03963pt too wide) in paragraph at lines 9771--9771 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [114 [22]] [425] [38] Chapter 7 [39] Underfull \hbox (badness 4048) in paragraph at lines 29148--29153 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29148--29153 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29148--29153 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [426] [115] [23 [427]] [428] [24 [429] [116 Chapter 6] [25]] [430] Chapter 8 [26 [40 [431]] [117]] [41] [432] Chapter 9 [42 [118]] [433] [27] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29686--29686 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [434 [43]] [28] Chapter 7 [29] [435 Chapter 10] [44] [436 [30]] [437 [31] Chapter 8 [119] [32]] Overfull \hbox (13.9408pt too wide) in paragraph at lines 29970--29972 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [438] [45 [439]] [33 Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] Underfull \hbox (badness 7558) in paragraph at lines 30186--30190 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 30196--30198 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the [440] <./images/hist.pdf>] [34] <./images/ecdf.pdf> <./images/QQ.p df> [35] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10329--10329 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [120 [47 [36]] Underfull \hbox (badness 5417) in paragraph at lines 30201--30204 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30205--30207 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30208--30210 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [441] <./images/ice.pdf> [37]] [442 [38]] Chapter 9 [39] [443 [48]] [121] [444] [40] [49 [445] Chapter 10 [41]] [446] [42] [50] [43] Underfull \hbox (badness 10000) in paragraph at lines 30615--30619 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [447] (Function and Variable Index) [51] [44 (./R-lang.vrs] [122] [45] [448 [46]] [47] [123 [52] [48]] [49]) Chapter 11 (Concept Index) [50] [53] [449 (./R-lang.cps] [124 [51])] Appendix A [54] [125 [55] [450 ) (see the transcript file for additional information) [53 [451 [54] Output written on R-lang.pdf (60 pages, 409696 bytes). Transcript written on R-lang.log. [55] [128 [452]] [453 [56]] [454] [57] Underfull \hbox (badness 10000) in paragraph at lines 11162--11164 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [129] [58] [59 [455]] [130 [456]] [60] [131] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31300--31300 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [457] [61 [132]] Chapter 12 [62 [458]] [133] Underfull \hbox (badness 10000) in paragraph at lines 31431--31435 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31431--31435 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [459] [134] [460 [63]] [135] [136 [461] [64]] [137] Underfull \hbox (badness 2302) in paragraph at lines 31671--31678 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [462 [65]]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [138] [66entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: Overfull \hbox (12.78088pt too wide) in paragraph at lines 31723--31723 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [463] pdf,] fonts, Underfull \hbox (badness 1158) in paragraph at lines 31827--31832 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [464] markup, glyphs, [67 page headings, tables, conditionals, indexing,] sectioning, [139 toc, environments, defuns, Underfull \hbox (badness 10000) in paragraph at lines 31854--31860 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 31854--31860 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [465 macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> )] localization,] Underfull \hbox (badness 10000) in paragraph at lines 31930--31935 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 31930--31935 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [466 formatting,] and turning on texinfo input format.) (./R-admin.aux [68] [140 Overfull \hbox (15.18042pt too wide) in paragraph at lines 32012--32012 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [467]] [69] [70 Overfull \hbox (22.06111pt too wide) in paragraph at lines 12183--12183 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [141]] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72 [468 [142] [73]]] Chapter 6 [143] [74] [75] [469] Chapter 13 [76] [144 Underfull \hbox (badness 2809) in paragraph at lines 32276--32282 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32283--32286 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [470]] [77] Chapter 14 [78] [471] [145 [79]] [472] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82 [473]]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [83] Appendix B [84]) [85 (./version.texi]) [146] [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [86] [474 [87]] [88] [89 [147]] [90] Appendix C [91] [92}]] Appendix D [93 [2]] [475 (./R-admin.toc [148 (./R-intro.vrs]] [-1 [94] [476] [149] [-2]]) [477 [-3 [95]] (./R-admin.toc) [478] (./R-admin.toc]) [479 Chapter 1] [480]) [481 Appendix E] [96 [150] Underfull \hbox (badness 1735) in paragraph at lines 33087--33093 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [482 (./R-intro.cps]] Underfull \hbox (badness 4303) in paragraph at lines 33103--33106 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [483] [1] Chapter 2 [484 [2] [97] [485]]) Appendix F [98] [486] [151] [99 Overfull \hbox (66.78088pt too wide) in paragraph at lines 33421--33421 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [487]] ) (see the transcript file for additional information) < ] [152/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx7.pfb]> [153]] Underfull \hbox (badness 2512) in paragraph at lines 33730--33732 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [492 Overfull \hbox (15.18042pt too wide) in paragraph at lines 33826--33826 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:[] [493] [7]] [8 [496]] Warning: unbalanced parentheses in @def...< [499]]/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb> [10< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl9.pfb]> [11] Output written on R-intro.pdf (105 pages, 674425 bytes). Transcript written on R-intro.log. ] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34608--34608 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 34609--34609 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [504] [13 [505]] [159 [506] Underfull \hbox (badness 7685) in paragraph at lines 1285--1289 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14]] [507] Overfull \hbox (63.78036pt too wide) in paragraph at lines 34873--34873 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [508] [15 [160]] Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 34957--34967 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [509 Underfull \hbox (badness 10000) in paragraph at lines 13895--13901 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [161]] Underfull \hbox (badness 10000) in paragraph at lines 35001--35007 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35001--35007 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 35001--35007 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35013--35020 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35013--35020 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35013--35020 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [510 [162]] Underfull \hbox (badness 10000) in paragraph at lines 1502--1506 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16] [511] Chapter 8 [163] [17] Chapter 4 [18] [512This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] [513] [164 [19entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi] (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf,] [514] fonts, Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20] Chapter 5 [165 [21]] Chapter 6 [22] Underfull \hbox (badness 10000) in paragraph at lines 35311--35317 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [515 markup,] glyphs, [23] page headings, Overfull \hbox (22.06111pt too wide) in paragraph at lines 14306--14306 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [166 tables, conditionals,] [24 indexing, sectioning,] [516] toc, [25 environments,] defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, Overfull \hbox (33.55849pt too wide) in paragraph at lines 14354--14354 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [167] Underfull \hbox (badness 1163) in paragraph at lines 35499--35506 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 35499--35506 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [517 formatting, and turning on texinfo input format.) (./R-lang.aux [26 [168]]] [169] [27] [170] [518 [28] [171]] [172 [519]] Underfull \hbox (badness 10000) in paragraph at lines 14857--14864 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [173] [29 [174]] Underfull \hbox (badness 10000) in paragraph at lines 14980--14984 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [175] [30 (./R-exts.vrs] Chapter 7 [31] [520] Underfull \hbox (badness 1142) in paragraph at lines 35762--35768 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 35777--35777 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [521 [176] [32]] [522] [33] [177 Chapter 8 [34]] Chapter 9) [35 (Concept index) [178] [523]] (./R-exts.cps [36]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [37] Appendix A [524 [179 [38]) (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map]]) [180] ) (see the transcript file for additional information) } [2< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb]> [-1 (./R-lang.toc [41 [527) (./R-lang.toc] Chapter 2] Output written on R-exts.pdf (186 pages, 1100684 bytes). Transcript written on R-exts.log. [2] [42 [528]] [529 Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3]] [43] [44] [530] [4] [45] [531 [5]] [46] Appendix B [47] [6] Overfull \hbox (52.98038pt too wide) in paragraph at lines 36501--36501 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 36504--36504 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [532] [48] [7] [49] Underfull \hbox (badness 10000) in paragraph at lines 36555--36562 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 36555--36562 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [533] Chapter 3 [8] [50] [51] [9] [52] Appendix C [53] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36606--36606 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [534 [10] [54] [11 [55]] [12]] [56 [13]] [14] [535 [57]] [58] Overfull \hbox (56.55324pt too wide) in paragraph at lines 4957--4957 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 4995--4995 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [59 [15]] [536 [60] [16]] [61] [17] [62] [63 [18]] [19] [64] [65] [20] [66 Underfull \hbox (badness 2762) in paragraph at lines 36841--36850 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 36841--36850 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [537]] Chapter 4 [21] Overfull \hbox (31.3804pt too wide) in paragraph at lines 36903--36903 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [538] [67] Appendix D [68 [22] Underfull \vbox (badness 7777) has occurred while \output is active [539]] [69] [23 [540]] [70] (Function and variable index) [71] (./R-admin.vrs) (Concept index) Overfull \hbox (4.38043pt too wide) in paragraph at lines 37068--37068 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [541 [72]] (./R-admin.cps) (Environment variable index) [73] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37106--37106 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 3219) in paragraph at lines 37155--37160 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37155--37160 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [542] (./R-admin.ens [24]) Underfull \hbox (badness 2452) in paragraph at lines 37245--37248 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37245--37248 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [543] [74] Chapter 5 [25 ) (see the transcript file for additional information)] [547 [31] [551 Underfull \hbox (badness 1082) in paragraph at lines 37778--37781 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [552] [553] [34 Output written on R-admin.pdf (79 pages, 555640 bytes). Transcript written on R-admin.log. Underfull \hbox (badness 1038) in paragraph at lines 37965--37968 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [554]] [555] [35 [556]] [557] [558 [36]] Underfull \hbox (badness 1515) in paragraph at lines 38304--38307 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [559] [37] [560] [38] Chapter 7 [561] [39] Underfull \hbox (badness 4096) in paragraph at lines 38529--38532 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 38643--38647 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [564] [565] Chapter 8 [40] [41] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38794--38794 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 38796--38796 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 38798--38798 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] [566] Underfull \hbox (badness 10000) in paragraph at lines 38811--38813 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [567] Chapter 9 [42] Underfull \hbox (badness 10000) in paragraph at lines 38891--38894 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [568] [569 [43]]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Chapter 10 [44] Underfull \hbox (badness 1867) in paragraph at lines 39009--39013 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39071--39075 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [570]entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [571] pdf, fonts, [572] [45] [573] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46 markup,] [574 glyphs,] page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, [47 macros,] [575 cross references,] insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, Underfull \hbox (badness 1371) in paragraph at lines 39431--39435 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 TZ \T1/ptm/m/n/10 is set but empty or in-val id, most plat-forms de-fault to `\T1/pcr/m/n/10 UTC\T1/ptm/m/n/10 ', the time z one col- Underfull \hbox (badness 1648) in paragraph at lines 39431--39435 \T1/ptm/m/n/10 lo-qui-ally known as `\T1/pcr/m/n/10 GMT\T1/ptm/m/n/10 ' (see [] []$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Coordinated _ [576] [48] Underfull \hbox (badness 5637) in paragraph at lines 39504--39513 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the Ol-son/IANA Underfull \hbox (badness 1629) in paragraph at lines 39504--39513 \T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion in the file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 39514--39521 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 39514--39521 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 39514--39521 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [577 formatting, and turning on texinfo input format.) (./R-exts.aux ] [49] [578] [50 [579]] (Function and Variable Index) [51 [580] (./R-lang.vrs] Underfull \hbox (badness 10000) in paragraph at lines 39798--39800 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [581] [52 Overfull \hbox (15.18042pt too wide) in paragraph at lines 39920--39920 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39922--39922 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [582]] [583]) (Concept Index) [53] (./R-lang.cps [584]) Appendix A [54 [585]] [586] [55] ) (see the transcript file for additional information) [588] Output written on R-lang.pdf (60 pages, 409696 bytes). Transcript written on R-lang.log. Underfull \hbox (badness 3460) in paragraph at lines 40424--40427 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 40431--40439 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 40431--40439 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less Underfull \hbox (badness 10000) in paragraph at lines 40440--40444 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 40440--40444 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 40440--40444 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 40461--40466 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [590] Underfull \hbox (badness 3895) in paragraph at lines 40523--40535 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 40523--40535 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [591] [592] [593] Underfull \hbox (badness 10000) in paragraph at lines 40708--40711 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [594] [595] Overfull \hbox (9.78043pt too wide) in paragraph at lines 40845--40845 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [596] [597] [598]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [599]) (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [600] [601}]] [2] (./R-exts.toc [-1 [602]] Underfull \hbox (badness 1803) in paragraph at lines 41396--41399 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), [603] [-2 Underfull \hbox (badness 2334) in paragraph at lines 41400--41407 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 4726) in paragraph at lines 41426--41430 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 41426--41430 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [604]] [605] [-3] [606]) [-4] (./R-exts.toc) Underfull \hbox (badness 3668) in paragraph at lines 41615--41617 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [607 (./R-exts.toc]) (Acknowledgements) Chapter 1 [1] [608] [2] [609] [3] [610] [4] Underfull \hbox (badness 6220) in paragraph at lines 41897--41902 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 41897--41902 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 41897--41902 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 41913--41918 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 1603) in paragraph at lines 41932--41936 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [611 [5]] Underfull \hbox (badness 10000) in paragraph at lines 41997--42000 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 41997--42000 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42003--42009 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and [612 Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6]] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42038--42038 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [613] Underfull \hbox (badness 1622) in paragraph at lines 42116--42118 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [614 [7] [615]] [8 [616]] [617] [9] Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [618] [10] Underfull \hbox (badness 2846) in paragraph at lines 42470--42474 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [619 [11]] [12 Overfull \hbox (4.38043pt too wide) in paragraph at lines 42510--42510 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 42531--42535 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [620]]) (./compiler-pkg.tex Chapter 2. [621 [13]] [622 [14]] [623] [624]) (./datasets-pkg.tex [15 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [625]] [626] [16 [627]] [17 [628]] [18] [629] Overfull \hbox (15.18042pt too wide) in paragraph at lines 294--294 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [630 [19]] Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [631] [20] [632] [21] [633 [22]] [634] [23] [635] [24] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2231--2231 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2233--2233 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [25 Overfull \hbox (66.81013pt too wide) in paragraph at lines 691--694 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [636]] [26] [27] [637 Underfull \hbox (badness 10000) in paragraph at lines 2482--2484 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [28]] [29 Overfull \hbox (66.81013pt too wide) in paragraph at lines 824--827 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [638]] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2605--2605 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [30] [31] [639] [32] [640] [33] [641] [34] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [642] [35] [643] [36] [644] [37] [38 [645]] [39] [646] [40] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [647] [41] [42 [648]] [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 1525--1528 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1525--1528 \T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m /n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a bove [649] [45] Underfull \hbox (badness 1325) in paragraph at lines 1606--1611 []\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [650] [46] [47] [651] [48] [49] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1713--1716 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [652] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1815--1815 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [653 [50]] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4536--4536 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4538--4538 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4539--4539 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] [51] [52 [654]] [53] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1931--1931 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1932--1932 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [655] [54] [656] [55] [657 [56]] [57] [658] [58] [59] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2135--2138 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [659] [60] [660] [61] [661] [662] [62] Chapter 2 [63] [663] [64] [664] [65] [66] [665] [67] [666] [68] [69] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2676--2679 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [667] [70] Overfull \vbox (13.87083pt too high) has occurred while \output is active [668] [71] Underfull \vbox (badness 1789) has occurred while \output is active [669] [670 [72]] Overfull \vbox (12.25539pt too high) has occurred while \output is active [671] [73] [672] [74] Overfull \vbox (17.12102pt too high) has occurred while \output is active [673] Underfull \hbox (badness 10000) in paragraph at lines 6585--6592 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [75] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3105--3105 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [674] [76] [675] Underfull \hbox (badness 10000) in paragraph at lines 6762--6768 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [77] [676] [78] [677] [79] [678 [80]] Chapter 3 [81] [679] [82] [83] [680] [84] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3562--3562 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [681] [85] [682] [86] [87] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3710--3713 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [683] [88] Chapter 4 [89 Overfull \vbox (10.49593pt too high) has occurred while \output is active [684]] [90] Underfull \hbox (badness 1173) in paragraph at lines 3844--3848 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [685 [91]] [92] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3919--3919 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3948--3951 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / [686 [93]] Underfull \hbox (badness 10000) in paragraph at lines 8057--8066 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [94] [687] [688] [95] [689] [96 [690]] [691] [692] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8335--8336 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [97] [693] [694] [98 [695]] [696] [697] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8467--8467 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8495--8497 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [99] [698] [699]) (./grDevices-pkg.tex [700] Chapter 4. [701] [702 Overfull \hbox (50.80455pt too wide) in paragraph at lines 8626--8626 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [100]] [703] [101] [704] [102 [705]] [103 [706]] Chapter 5 [104] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [707] Overfull \hbox (6.78088pt too wide) in paragraph at lines 470--470 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [708] [709] [710 [105]] [711] [106] [712] [713] [714 [107]] [715] [108 [716]] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [717] [109] Underfull \hbox (badness 1325) in paragraph at lines 1131--1137 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [718] [110] Underfull \hbox (badness 10000) in paragraph at lines 1172--1174 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [719] [111 Overfull \hbox (25.98041pt too wide) in paragraph at lines 1224--1224 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [720]] [112] Underfull \hbox (badness 1173) in paragraph at lines 1266--1269 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [721] [113] [722 Overfull \hbox (30.03963pt too wide) in paragraph at lines 9771--9771 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [114]] [115] [723] Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1526--1529 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [724] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [725] [116] [726] [117] [727] Underfull \hbox (badness 1565) in paragraph at lines 1754--1759 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1754--1759 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [728 [118]] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1837--1837 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [729] [119] Underfull \hbox (badness 1184) in paragraph at lines 1878--1888 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1878--1888 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [730 Overfull \hbox (16.31242pt too wide) in paragraph at lines 10329--10329 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [120]] [121] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [731] [122] [123] [732] [124 Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [733]] [125] [734] [126] Underfull \hbox (badness 2326) in paragraph at lines 2254--2264 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2254--2264 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2254--2264 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2254--2264 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [735] [127] [736] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2357--2357 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [737] [738] [128] [739] Underfull \hbox (badness 10000) in paragraph at lines 11162--11164 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [129] [740] [130] [741 [131]] [742] [132] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [743] [744 [133]] [134] [745] [135] [746] [136] [137 [747]] [748 [138]] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3138--3138 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3139--3139 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3170--3172 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [749] [139] Underfull \hbox (badness 10000) in paragraph at lines 3230--3235 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [750] [140 [751]] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12183--12183 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [141] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3382--3382 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [752] [142 [753]] Chapter 6 [143] Underfull \hbox (badness 3525) in paragraph at lines 3489--3492 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 1968) in paragraph at lines 3503--3505 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [754] [144] [145] [755] [756 [146]] [147] [757] [148] [149] Underfull \hbox (badness 5939) in paragraph at lines 3797--3802 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [758] [759] [150] [760] [151] [761] [762 [152]] [153] [763] [154] Underfull \hbox (badness 7576) in paragraph at lines 4170--4177 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4170--4177 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [764] [765] [155] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4287--4287 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] Underfull \hbox (badness 1502) in paragraph at lines 4334--4339 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [766 Warning: unbalanced parentheses in @def...] [156 [767]] [157] Underfull \hbox (badness 4765) in paragraph at lines 4493--4495 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if [768 [158]] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4507--4507 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 5077) in paragraph at lines 4547--4553 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [769] [159] [160] Underfull \hbox (badness 10000) in paragraph at lines 13895--13901 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [161] [162 Underfull \hbox (badness 1342) in paragraph at lines 4563--4565 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [770]] Chapter 8 [163] Underfull \hbox (badness 1874) in paragraph at lines 4640--4648 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [771 [164]] [165] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14306--14306 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [166] Underfull \hbox (badness 1755) in paragraph at lines 4707--4709 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [772 Overfull \hbox (33.55849pt too wide) in paragraph at lines 14354--14354 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [167]] [168] [773 [169]] [170 Underfull \hbox (badness 7344) in paragraph at lines 4878--4880 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4889--4893 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [774]] [171] [172] Underfull \hbox (badness 10000) in paragraph at lines 14857--14864 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [173 [775]] [174] Underfull \hbox (badness 10000) in paragraph at lines 14980--14984 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [175] (./R-exts.vrs Underfull \hbox (badness 1552) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5012--5014 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5044--5050 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [776] [176 Underfull \hbox (badness 10000) in paragraph at lines 5070--5077 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [777]] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5171--5171 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [778 [177]] [779]) (Concept index) [178 Overfull \hbox (6.78088pt too wide) in paragraph at lines 5283--5283 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5289--5293 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [780]] (./R-exts.cps Underfull \hbox (badness 10000) in paragraph at lines 5369--5371 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [781] [179] Underfull \hbox (badness 1072) in paragraph at lines 5405--5411 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [782) [180]] ) (see the transcript file for additional information) < /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb> [784 Output written on R-exts.pdf (186 pages, 1100680 bytes). Transcript written on R-exts.log. [786] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5728--5728 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5741--5744 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 1189) in paragraph at lines 6138--6140 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 6236--6238 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6275--6282 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 6275--6282 \T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s ys-tems which have the Wine [795] Underfull \hbox (badness 3088) in paragraph at lines 6359--6363 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [796] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6404--6404 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] Underfull \hbox (badness 10000) in paragraph at lines 6436--6439 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [797] [798] Underfull \hbox (badness 5637) in paragraph at lines 6527--6533 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6560--6563 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [799] [800] [801] Underfull \hbox (badness 6157) in paragraph at lines 6717--6720 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6728--6730 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [802] [803] [804]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [805] [806] [807] [808] Underfull \hbox (badness 1412) in paragraph at lines 286--291 []\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [809] [810] [811] Underfull \hbox (badness 2726) in paragraph at lines 465--471 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [812] [813] [814] Underfull \hbox (badness 10000) in paragraph at lines 655--659 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 655--659 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if Underfull \hbox (badness 2735) in paragraph at lines 683--690 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [815] Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [816] [817] Underfull \hbox (badness 1062) in paragraph at lines 849--852 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [818] [819] [820] [821] [822]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: [823 pdf, fonts,] markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, [824 defuns, macros, cross references, insertions,] (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, Overfull \hbox (0.78088pt too wide) in paragraph at lines 1283--1283 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [825] formatting, and turning on texinfo input format.) 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The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1362--1364 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1384--1388 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [826] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1432--1432 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1433--1433 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1440--1440 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [827] [828] [829] [830] [831] Underfull \hbox (badness 10000) in paragraph at lines 1740--1746 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [832] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1786--1786 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [833] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1869--1869 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [834] [835] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1998--1998 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2003--2003 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [836] [837] [838] [839] [840] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [841] [842] [843] [844] [845] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2617--2617 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [846] [847] Underfull \hbox (badness 5878) in paragraph at lines 2778--2782 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2803--2806 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [848] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2831--2831 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2835--2835 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [849] Underfull \hbox (badness 10000) in paragraph at lines 2887--2890 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [850] [851] [852] [853] Underfull \hbox (badness 1755) in paragraph at lines 3148--3152 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [854] Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [855] [856)] (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [857]) (./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map Overfull \hbox (25.98041pt too wide) in paragraph at lines 3406--3406 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3425--3425 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3429--3429 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [858] [859}]] [2] (./R-exts.toc [860] [-1 Overfull \hbox (36.7804pt too wide) in paragraph at lines 3606--3606 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3607--3607 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3644--3644 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [861]] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3696--3696 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Underfull \vbox (badness 10000) has occurred while \output is active [862] [-2] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3716--3716 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3779--3783 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for [863] [-3] [864) [-4]] (./R-exts.toc [865]) (./R-exts.toc Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [866)] (Acknowledgements) Chapter 1 [867] [1] Underfull \hbox (badness 3930) in paragraph at lines 4094--4096 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [868] [2] [869] [870] [871] [3 Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [872]] [4] Underfull \hbox (badness 1286) in paragraph at lines 4402--4405 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4500--4500 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor)[] [874 [5]] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4504--4504 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [875] Underfull \hbox (badness 1264) in paragraph at lines 4622--4635 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [876] [7] [877] [8 Underfull \hbox (badness 7925) in paragraph at lines 4759--4765 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. [878]] [879] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [9 [880 ] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 ] [881 ] [10] [882] [11] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [883 [12]] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5197--5197 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5198--5198 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [884] [13] [14] [885] [15] [16] [17 Underfull \hbox (badness 3954) in paragraph at lines 5299--5302 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5355--5359 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [886] [18]] [19] [20] [887] [21] [888] [22] [889] [23 Overfull \hbox (9.78043pt too wide) in paragraph at lines 5563--5563 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5564--5564 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5615--5619 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., Underfull \hbox (badness 1024) in paragraph at lines 5615--5619 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [890]] [24 [891]] [892] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2231--2231 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2233--2233 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [25] [893] [26 [894]] [27] [895] Underfull \hbox (badness 10000) in paragraph at lines 2482--2484 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [28] [896] [29] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2605--2605 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [30] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6048--6048 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [897] [31] [898] [32] [899] [33] [900] [34] [901] [35] [902 [36]] [37] Underfull \hbox (badness 10000) in paragraph at lines 6475--6477 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [903] [38] [39] [904] [40] Underfull \hbox (badness 1028) in paragraph at lines 6569--6571 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of [41] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [905 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6706--6706 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [906 [42]] [43 Overfull \hbox (31.3804pt too wide) in paragraph at lines 6737--6737 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [907]] [44] [908 [45]] [46 Underfull \hbox (badness 10000) in paragraph at lines 6859--6861 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6886--6886 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6892--6892 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [909]] [47] Underfull \hbox (badness 2600) in paragraph at lines 6952--6954 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [910] [48 [911]] [49] [912] Underfull \hbox (badness 1881) in paragraph at lines 7141--7146 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [913] [50] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7184--7184 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [914] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4536--4536 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4538--4538 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4539--4539 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] [51] [52 [915]] [916 [53]] [917 [54]] [55] [56] [918 [57]] [58] [919] [59] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7571--7571 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7575--7575 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [920] [60] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7587--7587 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [921] [922 [61]] [923] [62] Chapter 2 [924] [63] [64] [925 [65]] [66] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7930--7930 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [926 [67]] [68] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7937--7937 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [927] [69] [70 [928]] [71] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8108--8108 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8109--8109 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [929] [72] [930] [73] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8213--8213 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8224--8229 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [931 [74]] [932] Underfull \hbox (badness 10000) in paragraph at lines 6585--6592 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [75 Overfull \hbox (20.58041pt too wide) in paragraph at lines 8328--8328 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8343--8343 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [933]] [934] [76] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [935] [936] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8647--8647 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [937] Underfull \hbox (badness 10000) in paragraph at lines 6762--6768 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [77] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8709--8715 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [938] [78]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [939] Underfull \hbox (badness 1205) in paragraph at lines 8822--8824 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [940] [941] [79 Overfull \hbox (25.98041pt too wide) in paragraph at lines 8941--8941 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [942]) (./grid-pkg.tex] Chapter 6. [943] [944] [80] [945] [946] Chapter 3 [81] [947] [82] [948] [83] Underfull \hbox (badness 10000) in paragraph at lines 383--389 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 383--389 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [949] [84] [950] [85 [951]] [86] [87 [952]] [88] [953 Chapter 4 [89]] [90 [954]] [91] [92] [955] [93] [956] [957] Underfull \hbox (badness 10000) in paragraph at lines 8057--8066 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [94] [958] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1023--1023 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [959] [95] Underfull \hbox (badness 1430) in paragraph at lines 1072--1077 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [960] [96] [961] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8335--8336 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [97 [962]] Underfull \hbox (badness 3219) in paragraph at lines 1286--1289 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [963] [98] [964] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8467--8467 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8495--8497 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [99 [965]] [966] [967] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8626--8626 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [100] [101] [968 [102]] [103] Chapter 5 [104] [969] [105] [106 Overfull \hbox (9.78043pt too wide) in paragraph at lines 1673--1673 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [970]] [107] [108] [109] [971] [110] [972] [111 Overfull \hbox (25.98041pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1888--1888 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [973]] Underfull \hbox (badness 2961) in paragraph at lines 1924--1929 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [974 [112]] Underfull \hbox (badness 1430) in paragraph at lines 1983--1988 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2012--2015 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [975] [113] Overfull \hbox (30.03963pt too wide) in paragraph at lines 9771--9771 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [114 [976]] [977] [115] Underfull \hbox (badness 2894) in paragraph at lines 2219--2226 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [978] [116] [979 [117]] [118 [980]] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2375--2375 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2387--2392 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [981] [119] [982] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10329--10329 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [120] [121] [983] [122 Overfull \hbox (15.18042pt too wide) in paragraph at lines 2580--2580 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2612--2612 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [984]] [123] [985] [124 [986]] [125 [987]] [126] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2852--2852 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [988] [127] [989] [128] [990] Underfull \hbox (badness 10000) in paragraph at lines 11162--11164 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [129] [991] [130 [992]] [131] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3162--3162 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [993] [132] [133] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3258--3258 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [994] [134] [135] Underfull \hbox (badness 2799) in paragraph at lines 3292--3298 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [995] [136] [137] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3384--3384 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [996] [138] [139] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3391--3391 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [997] [140] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12183--12183 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [141] [998 [142]] Chapter 6 [143] [144 [999]] [145 Overfull \hbox (9.78043pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3600--3600 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1000]] [146] [147] [1001] [148] [149 [1002]] [1003 [150]] [1004 [151]] [1005] [152] [1006] [153] [154] [1007] [155] Warning: unbalanced parentheses in @def... [1008] [156] [157] Underfull \hbox (badness 1430) in paragraph at lines 4157--4162 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1009] [158] [159] [1010] [160] Underfull \hbox (badness 10000) in paragraph at lines 13895--13901 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [161] [162] [1011 Chapter 8 [163]] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1012 [164]] [165] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14306--14306 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [166] Underfull \hbox (badness 1430) in paragraph at lines 4386--4391 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1013 Overfull \hbox (33.55849pt too wide) in paragraph at lines 14354--14354 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [167]] [168] [1014 [169]] [170] [1015] [171] [172] Underfull \hbox (badness 10000) in paragraph at lines 14857--14864 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [173] [174 Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1016] Underfull \hbox (badness 10000) in paragraph at lines 14980--14984 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index)] [175] (./R-exts.vrs [1017] [176] [1018] [177 [1019]]) (Concept index) [1020 [178]] (./R-exts.cps [1021] [179]) [180] ) (see the transcript file for additional information) < /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb> Underfull \hbox (badness 10000) in paragraph at lines 5174--5176 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1025 Output written on R-exts.pdf (186 pages, 1100680 bytes). Transcript written on R-exts.log. ] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] Underfull \hbox (badness 3449) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1036] [1037] [1038] [1039] [1040] Underfull \hbox (badness 1867) in paragraph at lines 6172--6174 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 6209--6215 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1041] [1042] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1043] [1044] [1045] [1046] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6545--6545 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1047]) (./methods-pkg.tex [1048] Chapter 7. [1049] [1050] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1051] [1052] [1053] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1054] [1055] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1056] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1057] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1058] [1059] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1795--1795 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1797--1797 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1073] [1074] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1075] [1076] [1077] Underfull \hbox (badness 1132) in paragraph at lines 2215--2220 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1078] [1079] Underfull \hbox (badness 10000) in paragraph at lines 2329--2333 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2361--2361 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1080] [1081] [1082] Underfull \hbox (badness 3792) in paragraph at lines 2575--2578 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2606--2610 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1083] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2662--2662 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1084] [1085] [1086] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2881--2881 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1087] [1088] [1089] [1090] [1091] [1092] [1093] Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3404--3409 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1094] [1095] Underfull \hbox (badness 10000) in paragraph at lines 3532--3536 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1096] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3645--3654 [] [1097] [1098] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3765--3766 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 Underfull \hbox (badness 10000) in paragraph at lines 3812--3813 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1099] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3831--3832 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") Overfull \hbox (120.78088pt too wide) in paragraph at lines 3849--3850 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3911--3915 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 4138--4140 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1103] [1104] Underfull \hbox (badness 1629) in paragraph at lines 4250--4259 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4311--4311 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4312--4312 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4369--4369 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1107] [1108] Underfull \hbox (badness 1033) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1109] Underfull \hbox (badness 2126) in paragraph at lines 4577--4585 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1110] [1111] [1112] Underfull \hbox (badness 10000) in paragraph at lines 4814--4823 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1113] [1114] [1115] [1116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5198--5198 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1117] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5226--5226 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5240--5240 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1118] [1119] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1120] Underfull \hbox (badness 10000) in paragraph at lines 5466--5468 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1121] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1122] [1123] [1124] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1125] Underfull \hbox (badness 10000) in paragraph at lines 5760--5764 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5760--5764 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1126] Underfull \hbox (badness 10000) in paragraph at lines 5851--5855 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5851--5855 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1127] [1128] [1129] [1130] Underfull \hbox (badness 10000) in paragraph at lines 6213--6229 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1131] [1132] Underfull \hbox (badness 1248) in paragraph at lines 6346--6350 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6346--6350 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1133] Underfull \hbox (badness 4647) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1134] Underfull \hbox (badness 1072) in paragraph at lines 6578--6585 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1135] Underfull \hbox (badness 2875) in paragraph at lines 6650--6659 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6650--6659 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1136] Underfull \vbox (badness 10000) has occurred while \output is active [1137] [1138] [1139]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1140] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7012--7012 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7068--7075 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1141] [1142] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7203--7203 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1143]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1144] Underfull \hbox (badness 6708) in paragraph at lines 7312--7324 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7312--7324 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7312--7324 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1145] [1146] Underfull \hbox (badness 1694) in paragraph at lines 7475--7477 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7499--7502 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1147] [1148] Underfull \hbox (badness 10000) in paragraph at lines 7666--7673 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7666--7673 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] Underfull \hbox (badness 1052) in paragraph at lines 8492--8499 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1160] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8625--8625 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1161] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8700--8700 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1162] [1163] [1164] [1165] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1166] [1167] [1168] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9170--9170 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1169] [1170] Underfull \vbox (badness 2277) has occurred while \output is active [1171] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9432--9432 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1172] [1173] [1174] [1175] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9740--9740 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1176] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9850--9850 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1177] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9861--9861 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] Underfull \hbox (badness 10000) in paragraph at lines 10559--10561 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10567--10571 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1187] [1188] [1189] [1190]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1191] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1192] [1193] Underfull \hbox (badness 1024) in paragraph at lines 196--199 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1194] Underfull \hbox (badness 10000) in paragraph at lines 287--290 []\T1/ptm/m/n/10 Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.3.0 the de-fault wa s \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/10 ex-cept on Win-dows, but Underfull \hbox (badness 10000) in paragraph at lines 305--313 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1195] [1196] Underfull \hbox (badness 10000) in paragraph at lines 423--425 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1197] [1198] [1199] [1200] Underfull \hbox (badness 1917) in paragraph at lines 718--727 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 718--727 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1201] [1202] Underfull \hbox (badness 10000) in paragraph at lines 855--858 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1203] [1204] [1205] Underfull \hbox (badness 5388) in paragraph at lines 1048--1053 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from [1206] Underfull \hbox (badness 10000) in paragraph at lines 1072--1080 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1109--1109 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1207] [1208] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1225--1225 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1268--1271 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1209] Underfull \hbox (badness 3375) in paragraph at lines 1314--1316 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1210] [1211]) (./splines-pkg.tex [1212] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1213] [1214] [1215] [1216] [1217] [1218] [1219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1220] [1221] [1222] [1223] Overfull \hbox (25.98041pt too wide) in paragraph at lines 699--699 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1224] [1225] [1226]) (./stats-pkg.tex Chapter 10. [1227] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1228] [1229] [1230] [1231] [1232] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1233] [1234] [1235] [1236] [1237] [1238] [1239] Underfull \hbox (badness 1024) in paragraph at lines 848--850 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] Underfull \hbox (badness 10000) in paragraph at lines 1392--1394 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1248] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] Underfull \hbox (badness 10000) in paragraph at lines 2081--2086 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2081--2086 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2081--2086 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2087--2093 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2087--2093 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1258] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1259] [1260] [1261] [1262] Underfull \hbox (badness 1221) in paragraph at lines 2433--2438 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2433--2438 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1263] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1264] [1265] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2645--2645 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1266] [1267] [1268] [1269] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2885--2885 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1270] [1271] [1272] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3093--3095 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1273] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3140--3140 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3141--3141 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1274] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1275] [1276] [1277] [1278] [1279] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3531--3531 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1280] [1281] [1282] [1283] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3801--3801 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1284] [1285] [1286] [1287] [1288] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4086--4086 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4087--4087 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1289] [1290] [1291] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4322--4322 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1292] [1293] [1294] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4490--4490 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1295] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1296] [1297] [1298] [1299] [1300] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4942--4942 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4944--4944 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1301] [1302] Underfull \hbox (badness 7397) in paragraph at lines 5031--5035 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5031--5035 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1303] [1304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5165--5165 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5183--5183 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5210--5212 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by Underfull \hbox (badness 10000) in paragraph at lines 5215--5217 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1305] [1306] [1307] Underfull \hbox (badness 1436) in paragraph at lines 5393--5398 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5393--5398 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5393--5398 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1308] [1309] [1310] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5588--5588 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1311] Underfull \hbox (badness 1168) in paragraph at lines 5660--5665 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1312] [1313] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5754--5754 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1314] [1315] [1316] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5939--5939 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1317] [1318] Underfull \hbox (badness 10000) in paragraph at lines 6102--6107 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When [1319] [1320] [1321] Underfull \hbox (badness 5954) in paragraph at lines 6298--6300 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1322] Underfull \hbox (badness 2503) in paragraph at lines 6380--6383 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6384--6386 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6387--6392 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1323] Underfull \hbox (badness 7238) in paragraph at lines 6423--6426 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1324] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6458--6458 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6473--6473 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6488--6488 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1325] [1326] [1327] [1328] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6730--6730 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1329] [1330] Underfull \vbox (badness 10000) has occurred while \output is active [1331] [1332] [1333] [1334] Underfull \hbox (badness 10000) in paragraph at lines 7128--7132 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1335] Underfull \hbox (badness 6493) in paragraph at lines 7225--7228 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1336] [1337] Underfull \hbox (badness 10000) in paragraph at lines 7362--7365 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 10000) in paragraph at lines 7772--7777 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1344] [1345] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7910--7912 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1346] [1347] [1348] Underfull \hbox (badness 1210) in paragraph at lines 8127--8129 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1349] [1350] [1351] [1352] [1353] [1354] [1355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571 [] \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino mial()$mu_eta[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8593--8593 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8596--8596 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1356] [1357] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8734--8734 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1358] Underfull \hbox (badness 1859) in paragraph at lines 8773--8778 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1359] [1360] [1361] [1362] [1363] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9141--9141 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate S", "VeryS")))[] [1364] [1365] [1366] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2443) in paragraph at lines 9761--9767 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1373] [1374] [1375] Underfull \hbox (badness 3758) in paragraph at lines 9974--9977 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1376] [1377] [1378] [1379] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1380] Underfull \hbox (badness 4132) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1381] Underfull \hbox (badness 10000) in paragraph at lines 10377--10380 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1382] [1383] [1384] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1385] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1386] Underfull \hbox (badness 10000) in paragraph at lines 10700--10706 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10738--10743 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1387] [1388] Underfull \hbox (badness 2635) in paragraph at lines 10871--10874 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1389] [1390] [1391] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11073--11082 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1392] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11155--11155 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1393] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11188--11188 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11201--11205 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1394] [1395] [1396] Underfull \hbox (badness 7379) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1397] [1398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1399] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11587--11587 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11599--11599 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1400] Underfull \hbox (badness 1062) in paragraph at lines 11648--11653 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11665--11667 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1401] [1402] Underfull \hbox (badness 3623) in paragraph at lines 11816--11818 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1403] [1404] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11912--11912 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1405] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12005--12005 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1406] Underfull \hbox (badness 10000) in paragraph at lines 12053--12056 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1407] [1408] [1409] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1410] [1411] Underfull \hbox (badness 2753) in paragraph at lines 12345--12347 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1412] [1413] Underfull \hbox (badness 1292) in paragraph at lines 12470--12474 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1414] Underfull \hbox (badness 10000) in paragraph at lines 12583--12585 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12589--12593 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] Underfull \hbox (badness 4518) in paragraph at lines 13284--13289 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1426] [1427] [1428] Underfull \hbox (badness 10000) in paragraph at lines 13478--13482 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1429] [1430] Underfull \hbox (badness 6995) in paragraph at lines 13663--13665 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1431] [1432] [1433] Underfull \hbox (badness 1163) in paragraph at lines 13811--13819 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1434] Underfull \hbox (badness 4518) in paragraph at lines 13931--13936 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1435] [1436] Underfull \hbox (badness 10000) in paragraph at lines 14069--14073 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14069--14073 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1437] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14117--14117 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14118--14118 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1438] Underfull \hbox (badness 10000) in paragraph at lines 14173--14176 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14173--14176 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1439] [1440] [1441] [1442] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14459--14459 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14460--14460 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1443] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14510--14512 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14553--14553 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1444] [1445] [1446] [1447] [1448] [1449] [1450] Underfull \hbox (badness 2726) in paragraph at lines 14956--14959 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15671--15671 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1462] [1463] Underfull \hbox (badness 1014) in paragraph at lines 15809--15814 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1464] Underfull \hbox (badness 1648) in paragraph at lines 15869--15871 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 15883--15892 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 15883--15892 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1465] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15951--15951 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16504--16504 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1475] [1476] [1477] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16732--16732 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2772) in paragraph at lines 17167--17170 []\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate s. When Underfull \hbox (badness 10000) in paragraph at lines 17167--17170 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr /m/n/10 start \T1/ptm/m/n/10 is tried (if [1485] [1486] Underfull \hbox (badness 2359) in paragraph at lines 17287--17289 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1487] Underfull \vbox (badness 10000) has occurred while \output is active [1488] Underfull \vbox (badness 10000) has occurred while \output is active [1489] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17459--17459 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1490] Underfull \hbox (badness 10000) in paragraph at lines 17539--17543 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1491] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17619--17619 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1492] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17666--17666 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17713--17713 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Underfull \hbox (badness 1248) in paragraph at lines 18203--18206 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1127) in paragraph at lines 18216--18220 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1501] Underfull \hbox (badness 1478) in paragraph at lines 18224--18228 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and Underfull \hbox (badness 2042) in paragraph at lines 18277--18279 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1502] [1503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18373--18373 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1504] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18415--18415 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18448--18448 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18451--18451 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1505] Underfull \hbox (badness 2564) in paragraph at lines 18486--18497 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18486--18497 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1506] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18549--18549 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1507] [1508] [1509] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18764--18764 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1510] Underfull \hbox (badness 1337) in paragraph at lines 18840--18843 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1511] [1512] [1513] [1514] [1515] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19156--19156 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1516] [1517] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19244--19244 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19247--19247 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1518] Underfull \hbox (badness 3049) in paragraph at lines 19326--19330 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1519] [1520] [1521] [1522] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19569--19569 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19576--19578 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19579--19582 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1523] Underfull \hbox (badness 1107) in paragraph at lines 19637--19639 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1524] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19692--19692 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1525] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19699--19699 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] Underfull \hbox (badness 10000) in paragraph at lines 19749--19752 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 19749--19752 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1526] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19793--19793 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1527] [1528] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19918--19918 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1529] Underfull \hbox (badness 10000) in paragraph at lines 19981--19983 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1530] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20029--20029 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) Underfull \hbox (badness 10000) in paragraph at lines 20084--20086 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1531] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20121--20121 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] Overfull \hbox (25.98041pt too wide) in paragraph at lines 20951--20951 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1545] Underfull \hbox (badness 6859) in paragraph at lines 21018--21025 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21029--21035 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Overfull \hbox (78.78088pt too wide) in paragraph at lines 22044--22044 [] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) %in % c("Pr(", "p-v"),[] [1562] [1563] [1564] [1565] [1566] Underfull \hbox (badness 1337) in paragraph at lines 22367--22373 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Overfull \hbox (133.98029pt too wide) in paragraph at lines 22912--22912 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1575] [1576] [1577] Underfull \hbox (badness 1028) in paragraph at lines 23052--23055 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1578] Underfull \hbox (badness 10000) in paragraph at lines 23162--23165 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23162--23165 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1579] Underfull \hbox (badness 10000) in paragraph at lines 23217--23219 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1580] Underfull \hbox (badness 10000) in paragraph at lines 23279--23281 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1581] [1582] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23381--23381 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1583] [1584] [1585] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23601--23601 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1586] [1587] Underfull \hbox (badness 10000) in paragraph at lines 23747--23750 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1588] Underfull \hbox (badness 2134) in paragraph at lines 23798--23802 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 23811--23811 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1589] [1590] [1591] [1592] [1593] [1594] [1595] Underfull \hbox (badness 2591) in paragraph at lines 24268--24274 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][ ][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/ ptm/m/n/10 mod-els (with ex-am- [1596] [1597] [1598] Underfull \hbox (badness 1867) in paragraph at lines 24465--24467 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1599] Underfull \hbox (badness 10000) in paragraph at lines 24478--24482 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24478--24482 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Overfull \hbox (20.58041pt too wide) in paragraph at lines 24514--24514 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1600] [1601] [1602] Underfull \hbox (badness 2495) in paragraph at lines 24704--24713 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1603] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24786--24786 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 24793--24795 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1604] [1605] Overfull \hbox (25.98041pt too wide) in paragraph at lines 24880--24880 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 24905--24905 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 24908--24908 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1606] Underfull \hbox (badness 10000) in paragraph at lines 24950--24955 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 24950--24955 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1607] Underfull \hbox (badness 2980) in paragraph at lines 25095--25097 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1608] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25131--25131 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] [1609] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25180--25180 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Underfull \vbox (badness 10000) has occurred while \output is active [1610] [1611] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25303--25303 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1612] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25370--25370 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1613] [1614] [1615] [1616] [1617] [1618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 25746--25746 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 25799--25802 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1619] [1620] Overfull \hbox (31.3804pt too wide) in paragraph at lines 25925--25925 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 25926--25926 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1621] Underfull \hbox (badness 2922) in paragraph at lines 25992--25997 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1622] Underfull \hbox (badness 2922) in paragraph at lines 26054--26059 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 3240) in paragraph at lines 26066--26070 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff [1623] Underfull \hbox (badness 2922) in paragraph at lines 26111--26116 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1624] Underfull \hbox (badness 2922) in paragraph at lines 26172--26178 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1625] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26194--26194 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26210--26210 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1626] [1627] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26324--26324 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) Overfull \hbox (4.38043pt too wide) in paragraph at lines 26347--26347 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response and gradient[] [1628] Underfull \hbox (badness 2922) in paragraph at lines 26385--26390 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1629] Underfull \hbox (badness 2922) in paragraph at lines 26441--26446 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 2922) in paragraph at lines 26499--26504 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1630] Underfull \hbox (badness 2922) in paragraph at lines 26554--26559 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26575--26575 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Underfull \hbox (badness 6493) in paragraph at lines 26623--26628 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1632] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26649--26649 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26651--26651 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1633] [1634] [1635] [1636] [1637] [1638] [1639] Underfull \hbox (badness 10000) in paragraph at lines 27147--27150 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27147--27150 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1640] [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 3396) in paragraph at lines 27576--27578 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1647] [1648] [1649] Underfull \hbox (badness 2237) in paragraph at lines 27753--27755 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1650] [1651] Underfull \hbox (badness 2591) in paragraph at lines 27917--27919 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1652] Underfull \hbox (badness 2237) in paragraph at lines 27963--27966 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1653] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28036--28036 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1654] [1655] Underfull \hbox (badness 3407) in paragraph at lines 28144--28148 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1656] [1657] Underfull \hbox (badness 1337) in paragraph at lines 28277--28281 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1658] [1659] Underfull \hbox (badness 10000) in paragraph at lines 28394--28397 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1660] [1661] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28523--28523 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28551--28551 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1662] Underfull \hbox (badness 1616) in paragraph at lines 28577--28580 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1663] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28656--28656 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1664] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28733--28733 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1665] Underfull \hbox (badness 5050) in paragraph at lines 28769--28774 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1666] Underfull \hbox (badness 2205) in paragraph at lines 28822--28827 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29417--29417 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1675] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29418--29418 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1676] [1677] [1678] [1679] Underfull \hbox (badness 10000) in paragraph at lines 29703--29707 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 29703--29707 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 29714--29714 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29715--29715 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1680] [1681] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29841--29841 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29850--29850 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] [1682] [1683] [1684] [1685] Underfull \hbox (badness 1337) in paragraph at lines 30067--30071 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] Underfull \hbox (badness 1337) in paragraph at lines 30551--30555 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1694] Underfull \hbox (badness 1946) in paragraph at lines 30628--30633 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 30650--30652 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1695] [1696] [1697] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30975--30975 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1700] Underfull \hbox (badness 6775) in paragraph at lines 31032--31037 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1701] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31095--31095 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31110--31110 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s parse = TRUE))[] [1702]) (./stats4-pkg.tex Chapter 11. [1703] [1704] [1705] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1706] [1707] [1708]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1709] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1710] [1711]) (./tcltk-pkg.tex [1712] Chapter 12. [1713] [1714] [1715] [1716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1717] [1718] [1719] Underfull \vbox (badness 10000) has occurred while \output is active [1720] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1732]) (./tools-pkg.tex Chapter 13. [1733] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1734] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1735] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1736] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1737] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1738] [1739] [1740] Underfull \hbox (badness 10000) in paragraph at lines 543--544 [][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer / en / opentype / [1741] [1742] [1743] [1744] [1745] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 905--905 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1747] Overfull \hbox (31.3804pt too wide) in paragraph at lines 953--953 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1748] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1749] [1750] Underfull \hbox (badness 5431) in paragraph at lines 1128--1131 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1751] Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1204--1207 []\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he r-it-ing from class [1752] [1753] Underfull \hbox (badness 10000) in paragraph at lines 1344--1347 []\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1754] [1755] [1756] [1757] [1758] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1667--1667 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1670--1670 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1677--1682 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1759] [1760] [1761]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1762] [1763] [1764] [1765] Underfull \hbox (badness 2644) in paragraph at lines 2149--2155 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgMacros \T1/ptm/m/n/10 func-tion firs t looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-age Overfull \hbox (101.58032pt too wide) in paragraph at lines 2183--2183 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1766] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2184--2184 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2211--2218 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2211--2218 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2211--2218 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1767] Underfull \hbox (badness 1342) in paragraph at lines 2263--2269 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1768] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2339--2339 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2352--2358 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1769] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2385--2385 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2394--2394 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2411--2411 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1770] [1771] [1772] [1773] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2676--2676 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1774] Underfull \hbox (badness 2486) in paragraph at lines 2721--2729 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1775] [1776] [1777] [1778] [1779] Underfull \hbox (badness 1072) in paragraph at lines 3099--3101 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1780] [1781] [1782] [1783] [1784] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3435--3435 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1785] [1786] [1787] [1788] Underfull \hbox (badness 4108) in paragraph at lines 3679--3686 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1789] [1790] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3779--3779 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3782--3782 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3816--3822 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1791] [1792] Underfull \hbox (badness 7832) in paragraph at lines 3938--3941 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1793] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4013--4013 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1794] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1795] [1796] [1797] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4210--4210 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4221--4224 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4237--4242 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4245--4251 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4245--4251 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1798] Underfull \hbox (badness 3758) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList \T1/ptm/m/n/10 ob- Underfull \hbox (badness 2865) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie d (for in-stance if there was [1799] [1800] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4457--4457 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4458--4458 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4470--4473 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', [1801] Underfull \hbox (badness 1742) in paragraph at lines 4474--4484 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4509--4515 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4509--4515 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 4537--4541 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1802] [1803] [1804]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1805] [1806] [1807] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1808] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1809] [1810] Underfull \hbox (badness 1946) in paragraph at lines 453--457 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1811] Overfull \hbox (0.78088pt too wide) in paragraph at lines 503--503 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 510--510 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 512--512 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] [1812] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 546--552 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1813] Underfull \hbox (badness 4505) in paragraph at lines 660--666 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1814] [1815] Underfull \hbox (badness 1603) in paragraph at lines 777--783 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 777--783 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1816] Overfull \hbox (6.78088pt too wide) in paragraph at lines 834--834 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1817] Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1818] Underfull \hbox (badness 10000) in paragraph at lines 1004--1007 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1819] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1087--1087 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1820] [1821] [1822] [1823] [1824] [1825] Underfull \hbox (badness 1859) in paragraph at lines 1458--1467 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1826] [1827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1559--1559 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1594--1594 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1828] [1829] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1740--1740 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1760--1760 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1830] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1816--1816 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1831] Underfull \hbox (badness 2213) in paragraph at lines 1857--1860 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1832] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via [1833] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1992--1992 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2015--2015 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1834] [1835] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2135--2135 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1836] Underfull \hbox (badness 1082) in paragraph at lines 2209--2213 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; Underfull \hbox (badness 10000) in paragraph at lines 2246--2248 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1837] Underfull \hbox (badness 1057) in paragraph at lines 2278--2285 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1838] [1839] [1840] Underfull \hbox (badness 10000) in paragraph at lines 2467--2469 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1841] [1842] [1843] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2703--2707 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1844] Underfull \hbox (badness 10000) in paragraph at lines 2757--2760 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set [1845] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2829--2829 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1846] Underfull \hbox (badness 2452) in paragraph at lines 2905--2908 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1847] [1848] [1849] [1850] [1851] [1852] [1853] Underfull \hbox (badness 1072) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1854] Underfull \hbox (badness 10000) in paragraph at lines 3441--3446 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3441--3446 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3441--3446 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1855] Underfull \hbox (badness 4660) in paragraph at lines 3563--3566 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to [1856] [1857] [1858] Underfull \hbox (badness 1565) in paragraph at lines 3772--3776 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of Underfull \hbox (badness 10000) in paragraph at lines 3793--3799 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1859] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3855--3855 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1860] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3883--3890 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1861] [1862] [1863] [1864] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4203--4203 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1865] [1866]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4274 ...mat Unordered and Ordered Lists}{format} [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1881] Underfull \hbox (badness 10000) in paragraph at lines 5311--5313 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1882] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1883] [1884] [1885] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1886] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 5612--5615 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1887] [1888] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1889] Underfull \hbox (badness 5091) in paragraph at lines 5870--5872 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL [1890] Overfull \hbox (44.55087pt too wide) in paragraph at lines 5886--5891 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 5899--5906 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1891] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., Underfull \hbox (badness 10000) in paragraph at lines 6016--6020 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , [1892] Underfull \hbox (badness 2376) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1314) in paragraph at lines 6089--6096 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1893] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6133--6133 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 6169--6173 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 6181--6184 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [1894] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6227--6227 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1895] [1896] Underfull \hbox (badness 4132) in paragraph at lines 6346--6348 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1897] [1898] [1899] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6504--6504 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1900] [1901] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6647--6647 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1902] Underfull \hbox (badness 10000) in paragraph at lines 6687--6689 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1903] [1904] Underfull \hbox (badness 10000) in paragraph at lines 6828--6830 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 6833--6835 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1905] [1906] [1907] Underfull \hbox (badness 1859) in paragraph at lines 7056--7059 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1908] Underfull \hbox (badness 1655) in paragraph at lines 7138--7141 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 7149--7149 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] [1909] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7153--7153 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 7161--7161 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1910] Underfull \hbox (badness 10000) in paragraph at lines 7246--7250 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1911] [1912] [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1915] [1916] [1917] Underfull \hbox (badness 10000) in paragraph at lines 7683--7688 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7683--7688 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 10000) in paragraph at lines 7690--7693 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7690--7693 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1918] [1919] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7806--7806 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7807--7807 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1920] [1921] [1922] [1923] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1924] Underfull \hbox (badness 10000) in paragraph at lines 8145--8149 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8145--8149 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1925] Underfull \hbox (badness 10000) in paragraph at lines 8258--8262 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8258--8262 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1926] [1927] Underfull \hbox (badness 10000) in paragraph at lines 8321--8325 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8321--8325 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1928] [1929] [1930] [1931] Underfull \hbox (badness 5203) in paragraph at lines 8652--8655 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1932] [1933] [1934] Underfull \hbox (badness 1776) in paragraph at lines 8878--8885 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set Overfull \hbox (30.78088pt too wide) in paragraph at lines 8902--8902 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1935] [1936] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9063--9063 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1937] [1938] [1939] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9244--9244 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [1940] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9330--9330 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] [1941] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9333--9333 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9338--9338 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1942] Underfull \hbox (badness 1077) in paragraph at lines 9410--9413 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [1943] [1944] [1945] [1946] [1947] [1948] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9850--9850 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1949] Underfull \hbox (badness 10000) in paragraph at lines 9937--9939 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1950] [1951] Underfull \hbox (badness 2181) in paragraph at lines 10060--10064 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10072--10076 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1952] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10090--10090 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10094--10094 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1953] [1954] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10226--10226 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1955] [1956] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10366--10366 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [1957] Underfull \hbox (badness 8075) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via Underfull \hbox (badness 6725) in paragraph at lines 10479--10488 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10479--10488 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10479--10488 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10479--10488 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1958] [1959] Underfull \hbox (badness 3646) in paragraph at lines 10605--10607 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [1960] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10643--10643 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1961] [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 10824--10828 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10855--10861 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1964] Underfull \hbox (badness 2012) in paragraph at lines 10950--10956 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use Underfull \hbox (badness 2096) in paragraph at lines 10963--10965 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 10966--10968 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10973--10976 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 10977--10980 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if [1965] Overfull \hbox (6.78088pt too wide) in paragraph at lines 11031--11031 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 11049--11060 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1966] [1967] Underfull \hbox (badness 2846) in paragraph at lines 11136--11146 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1968] [1969] Underfull \hbox (badness 10000) in paragraph at lines 11275--11278 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un- Underfull \hbox (badness 10000) in paragraph at lines 11275--11278 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11292--11295 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1970] [1971] Underfull \hbox (badness 2158) in paragraph at lines 11374--11377 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [1972] [1973] Underfull \hbox (badness 3333) in paragraph at lines 11557--11559 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [1974] [1975] [1976] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11722--11722 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 5970) in paragraph at lines 11755--11758 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11755--11758 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11766--11775 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1977] Overfull \hbox (36.7804pt too wide) in paragraph at lines 11810--11810 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [1978] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11841--11841 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 11848--11848 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11850--11850 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 12018--12020 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [1981] [1982] [1983] Underfull \hbox (badness 4492) in paragraph at lines 12175--12182 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12175--12182 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12175--12182 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [1984] [1985] Underfull \hbox (badness 2020) in paragraph at lines 12335--12351 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12335--12351 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [1986] Underfull \hbox (badness 5022) in paragraph at lines 12434--12438 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12441--12444 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 12441--12444 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] Underfull \hbox (badness 4467) in paragraph at lines 12950--12952 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 12963--12967 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to [1995] Overfull \hbox (36.87935pt too wide) in paragraph at lines 12977--12981 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 3557) in paragraph at lines 12983--12985 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12986--12988 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13037--13042 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with [1996] Underfull \hbox (badness 10000) in paragraph at lines 13045--13048 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13099--13099 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [1997] [1998] [1999] Underfull \hbox (badness 10000) in paragraph at lines 13287--13290 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; [2000] Overfull \hbox (42.18039pt too wide) in paragraph at lines 13303--13303 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13337--13337 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2001] Underfull \hbox (badness 1454) in paragraph at lines 13364--13368 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13389--13392 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and [2002] Underfull \hbox (badness 10000) in paragraph at lines 13434--13436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion Underfull \hbox (badness 3271) in paragraph at lines 13446--13450 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2003] [2004] [2005]) [2006] [2007] [2008] (./KernSmooth-pkg.tex Chapter 15. [2009] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2010] [2011] [2012] [2013] [2014] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2015] [2016] [2017] [2018]) (./MASS-pkg.tex Chapter 16. [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 7256) in paragraph at lines 1603--1605 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2415--2415 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2053] [2054] [2055] [2056] Underfull \hbox (badness 6559) in paragraph at lines 2693--2696 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2057] [2058] [2059] Underfull \hbox (badness 7362) in paragraph at lines 2863--2868 \T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 , Underfull \hbox (badness 3557) in paragraph at lines 2899--2907 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2899--2907 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2060] [2061] Underfull \hbox (badness 4686) in paragraph at lines 3031--3033 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 3045--3049 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2062] [2063] [2064] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3226--3226 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3233--3235 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2065] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1845) in paragraph at lines 4162--4164 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2078] [2079] [2080] [2081] [2082] [2083] [2084] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2085] [2086] Underfull \hbox (badness 10000) in paragraph at lines 4810--4813 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2087] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4888--4891 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2088] [2089] [2090] [2091] [2092] Underfull \hbox (badness 5681) in paragraph at lines 5288--5290 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5292--5295 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2093] Underfull \hbox (badness 1975) in paragraph at lines 5341--5343 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5927--5927 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2102] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5988--5988 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2103] [2104]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} [2105] Underfull \hbox (badness 1783) in paragraph at lines 6248--6252 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2106] [2107] [2108] [2109] Underfull \vbox (badness 10000) has occurred while \output is active [2110] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6546--6546 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2111] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2112] [2113] [2114] [2115] [2116] [2117] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7073--7073 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7090--7090 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7097--7104 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2118] Underfull \hbox (badness 10000) in paragraph at lines 7113--7115 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7168--7174 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2119] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7238--7238 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2120] [2121] Underfull \hbox (badness 5091) in paragraph at lines 7347--7350 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2122] [2123] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7477--7477 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2124] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7542--7542 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2125] [2126] [2127] [2128] [2129] [2130] Underfull \hbox (badness 4686) in paragraph at lines 7980--7982 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 7996--8000 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2131] [2132] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8099--8099 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8123--8127 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n /10 NA\T1/ptm/m/n/10 s are found. The [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9502--9502 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2153] Underfull \hbox (badness 1158) in paragraph at lines 9629--9632 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly), [2154] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9711--9711 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9713--9713 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9716--9716 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167]) (./Matrix-pkg.tex [2168] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2169] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2170] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2171] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2172] [2173] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2174] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2175] [2176] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2177] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2178] [2179] [2180] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2181] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2182]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2183pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] [2184] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2185] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2186] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2187] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2188] Underfull \hbox (badness 6445) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3861) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and [2189]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2190] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2191] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2192] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2193] [2194] [2195] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2196] [2197] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2198] Underfull \hbox (badness 4713) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2199] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2200] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2201] Underfull \hbox (badness 2707) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2202] Overfull \hbox (120.78088pt too wide) in paragraph at lines 2663--2663 []\T1/pcr/m/n/10 .symDiagonal(n, x = rep.int(1,n), uplo = "U", kind = if(is. logical(x)) "l" else "d")[] Overfull \hbox (120.78088pt too wide) in paragraph at lines 2664--2664 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind = if(is. logical(x)) "l" else "d")[] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2203] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2204] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 3803) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a [2205] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2206] [2207] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2208] Underfull \hbox (badness 1168) in paragraph at lines 3358--3361 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2209] [2210] Underfull \hbox (badness 4967) in paragraph at lines 3523--3527 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix", ...) \T1/ptm/m/n/10 or Overfull \hbox (2.39853pt too wide) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . [2211] Underfull \hbox (badness 6364) in paragraph at lines 3570--3573 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2212] [2213] Underfull \hbox (badness 10000) in paragraph at lines 3720--3725 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3720--3725 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 10000) in paragraph at lines 3730--3732 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3732--3735 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2214] Underfull \hbox (badness 10000) in paragraph at lines 3840--3843 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3840--3843 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the Underfull \hbox (badness 10000) in paragraph at lines 3843--3846 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3843--3846 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion [2215] Underfull \hbox (badness 6364) in paragraph at lines 3847--3850 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2216] Underfull \hbox (badness 4060) in paragraph at lines 3967--3970 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2217] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4007--4007 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4075--4079 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class [2218] Underfull \hbox (badness 10000) in paragraph at lines 4084--4087 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 4084--4087 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4089--4093 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2219] [2220] [2221] [2222] Underfull \hbox (badness 10000) in paragraph at lines 4377--4382 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2223] [2224] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4511--4511 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4514--4514 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4528--4528 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2225] [2226] Underfull \hbox (badness 10000) in paragraph at lines 4683--4685 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2227] [2228] Underfull \hbox (badness 10000) in paragraph at lines 4830--4835 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2229] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4911--4911 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4913--4913 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4917--4917 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4924--4924 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2230] [2231] Underfull \hbox (badness 4120) in paragraph at lines 5063--5066 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2232] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5100--5100 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5105--5105 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5112--5112 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5115--5115 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2233] Underfull \hbox (badness 1817) in paragraph at lines 5204--5213 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 5637) in paragraph at lines 5246--5248 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2234] Underfull \hbox (badness 3138) in paragraph at lines 5272--5274 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2235] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5339--5339 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] Underfull \hbox (badness 1603) in paragraph at lines 5360--5362 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2236] [2237] [2238] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5597--5597 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2239] Underfull \hbox (badness 10000) in paragraph at lines 5678--5681 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5689--5689 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2240] Underfull \hbox (badness 1622) in paragraph at lines 5726--5731 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5726--5731 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2241] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5787--5787 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5788--5788 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5795--5795 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2242] [2243] Underfull \hbox (badness 1062) in paragraph at lines 5924--5927 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 2809) in paragraph at lines 5953--5956 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2244] Underfull \hbox (badness 2635) in paragraph at lines 6065--6070 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6065--6070 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class [2245] Underfull \hbox (badness 10000) in paragraph at lines 6073--6076 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6183--6193 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6183--6193 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2246] Underfull \hbox (badness 1184) in paragraph at lines 6265--6268 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2247] Underfull \hbox (badness 10000) in paragraph at lines 6363--6366 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2248] Underfull \hbox (badness 10000) in paragraph at lines 6438--6441 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2249] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6454--6454 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Underfull \hbox (badness 2443) in paragraph at lines 6493--6499 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6493--6499 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6514--6517 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2250] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6584--6584 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2251] [2252] Underfull \hbox (badness 6268) in paragraph at lines 6720--6723 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2253] Underfull \hbox (badness 5036) in paragraph at lines 6744--6748 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6744--6748 \T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e mpty'' [][]sparse-Ma-trix[][][], as does [2254]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6837 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6917--6920 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6922--6925 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6922--6925 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6940--6943 Underfull \hbox (badness 7326) in paragraph at lines 6950--6952 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re -lies on a cor-rect [2255]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7013 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7121 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7221 ...tcrossprod}{matrix-products}{tcrossprod} [2256] Underfull \hbox (badness 1881) in paragraph at lines 7319--7325 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2257pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7381 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7381 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7392--7395 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 7392--7395 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7395--7400 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7404--7406 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7406--7408 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7410--7411 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2258] [2259] Underfull \hbox (badness 1062) in paragraph at lines 7591--7594 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2260] Underfull \hbox (badness 2809) in paragraph at lines 7625--7628 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2261] Underfull \hbox (badness 10000) in paragraph at lines 7677--7679 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter [2262] Underfull \hbox (badness 1406) in paragraph at lines 7717--7721 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7717--7721 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2263] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7815--7815 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2264] Underfull \hbox (badness 2635) in paragraph at lines 7880--7885 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7880--7885 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7888--7891 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2265] [2266] Underfull \hbox (badness 10000) in paragraph at lines 8082--8084 []\T1/ptm/m/n/10 fast [2267]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8122 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8122 \HeaderA{norm}{Matrix Norms}{norm} [2268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8209--8209 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8210--8210 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8211--8211 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8324--8334 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2269] Underfull \hbox (badness 1184) in paragraph at lines 8395--8398 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2270] Underfull \hbox (badness 10000) in paragraph at lines 8485--8488 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2271] Underfull \hbox (badness 10000) in paragraph at lines 8561--8564 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2272] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8577--8577 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2273] Underfull \hbox (badness 10000) in paragraph at lines 8687--8689 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8703--8705 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8709--8713 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2274] [2275] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8788--8788 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8793--8793 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8798--8798 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8821--8831 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8821--8831 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2276] [2277]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8922 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8968--8971 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 8995--8995 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] [2278] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9006--9006 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9024--9024 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9032--9032 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=1e-15))## just = X, incl. co rrect colnames[] [2279] Underfull \hbox (badness 10000) in paragraph at lines 9085--9091 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9102--9105 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2280] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9174--9174 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9195--9195 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9196--9196 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2281]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco nd}) has been already used, duplicate ignored \relax l.9215 ... the Reciprocal Condition Number}{rcond} [2282] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9328--9328 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2283] [2284] [2285] Underfull \hbox (badness 10000) in paragraph at lines 9511--9513 []\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably Underfull \hbox (badness 1325) in paragraph at lines 9517--9525 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2286] [2287] Underfull \hbox (badness 1558) in paragraph at lines 9662--9665 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2288] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9724--9724 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9728--9728 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2289]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9790 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9887--9887 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9892--9892 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2290] Underfull \hbox (badness 6047) in paragraph at lines 9927--9939 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9944--9947 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9949--9950 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9953--9960 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9953--9960 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 9966--9976 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 9966--9976 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2291] Underfull \hbox (badness 1194) in paragraph at lines 10000--10002 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10014--10017 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10023--10024 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10029--10031 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10033--10034 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10041--10044 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10059--10059 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10063--10063 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2292] Underfull \hbox (badness 10000) in paragraph at lines 10084--10087 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10112--10114 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10120--10123 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the [2293] Underfull \hbox (badness 10000) in paragraph at lines 10131--10135 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10131--10135 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10142--10144 []\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in -di-cat-ing if the re-sult must be a [2294] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10219--10219 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10220--10220 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10221--10221 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2295] [2296] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10405--10405 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10406--10406 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2297] Underfull \hbox (badness 4621) in paragraph at lines 10446--10450 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2298] Underfull \hbox (badness 10000) in paragraph at lines 10522--10525 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10534--10534 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10538--10538 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10539--10539 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10544--10544 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10547--10547 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2299] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10570--10570 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10571--10571 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10597--10597 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10599--10599 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10601--10601 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2300] Underfull \hbox (badness 10000) in paragraph at lines 10694--10702 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10715--10719 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2301] Underfull \hbox (badness 10000) in paragraph at lines 10745--10749 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10785 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2302] [2303] Underfull \hbox (badness 1430) in paragraph at lines 10915--10917 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10943--10943 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 10971--10973 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2304] Underfull \hbox (badness 2970) in paragraph at lines 11104--11110 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11104--11110 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2305] Underfull \hbox (badness 10000) in paragraph at lines 11155--11158 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11177--11180 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2306] Underfull \hbox (badness 10000) in paragraph at lines 11195--11200 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11210--11212 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2307] [2308] Underfull \hbox (badness 3525) in paragraph at lines 11328--11332 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11335--11341 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2309] Underfull \hbox (badness 10000) in paragraph at lines 11430--11434 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11430--11434 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11446--11451 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 1259) in paragraph at lines 11446--11451 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11454--11459 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2310] Underfull \hbox (badness 2057) in paragraph at lines 11526--11528 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2311] [2312] Underfull \hbox (badness 6641) in paragraph at lines 11612--11615 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11652--11656 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11652--11656 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2313] Underfull \hbox (badness 7649) in paragraph at lines 11759--11761 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2314] [2315] [2316] Underfull \hbox (badness 7362) in paragraph at lines 11960--11962 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2317] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11998--11998 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11999--11999 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2318] [2319] Underfull \hbox (badness 6910) in paragraph at lines 12249--12251 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2320] [2321] [2322]) (./boot-pkg.tex Chapter 18. [2323] [2324] [2325] [2326] [2327] [2328] [2329] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2330] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2331] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2332] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2333] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2334] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2335] [2336] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues [2337] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2338] [2339] [2340] [2341] [2342] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2343] [2344] [2345] [2346] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2347] [2348] [2349] [2350] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] Underfull \vbox (badness 10000) has occurred while \output is active [2351] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2352] [2353] [2354] [2355] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. [2356] Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2357] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2358] [2359] [2360] [2361] [2362] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2363] [2364] [2365] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2366] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2367] [2368] [2369] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2370] [2371] [2372] [2373] [2374] [2375] [2376] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2377] [2378] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2379] [2380] [2381] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2383] [2384] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2385] [2386] [2387] [2388] [2389] [2390] [2391] [2392] [2393] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2394] [2395] [2396] [2397] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2399] [2400] [2401] [2402] [2403] [2404] [2405] [2406] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2407] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2408] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2409] [2410] [2411] [2412] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2413] [2414] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2415] [2416] [2417] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2418] [2419] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427]) (./class-pkg.tex [2428] Chapter 19. [2429] [2430] [2431] [2432] [2433] [2434] [2435] [2436] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2437] [2438] [2439] [2440] [2441] [2442] [2443] [2444]) (./cluster-pkg.tex Chapter 20. [2445] Underfull \hbox (badness 3098) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2446] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2447] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2448] [2449] Underfull \vbox (badness 10000) has occurred while \output is active [2450] [2451] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2452] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2453] Overfull \hbox (66.78088pt too wide) in paragraph at lines 636--636 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2454] Underfull \hbox (badness 3078) in paragraph at lines 682--685 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2455] Underfull \hbox (badness 2941) in paragraph at lines 771--774 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2456] Overfull \hbox (9.78043pt too wide) in paragraph at lines 809--809 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2457] Underfull \hbox (badness 10000) in paragraph at lines 857--859 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2458] Overfull \hbox (24.78088pt too wide) in paragraph at lines 922--922 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2459] Underfull \hbox (badness 4872) in paragraph at lines 968--970 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 982--986 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2460] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1089--1089 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2461] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1144--1144 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2462] Underfull \hbox (badness 4144) in paragraph at lines 1176--1180 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2463] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1252--1252 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1258--1258 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2464] [2465] Underfull \hbox (badness 10000) in paragraph at lines 1397--1402 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*, cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1445--1448 Underfull \hbox (badness 10000) in paragraph at lines 1462--1466 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , [2466] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1486--1486 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1496--1496 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2467] Underfull \hbox (badness 5741) in paragraph at lines 1536--1539 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1602--1602 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2469] Underfull \hbox (badness 5008) in paragraph at lines 1719--1727 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where [2470] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1810--1810 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] [2471] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1829--1829 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2472] [2473] [2474] [2475] Underfull \hbox (badness 10000) in paragraph at lines 2137--2139 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2148--2151 Underfull \hbox (badness 3179) in paragraph at lines 2162--2168 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2476] [2477] [2478] Underfull \hbox (badness 10000) in paragraph at lines 2320--2323 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2479] Underfull \hbox (badness 1292) in paragraph at lines 2388--2391 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2397--2399 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2420--2423 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2480] [2481] [2482] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2634--2634 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2483] [2484] [2485] Underfull \hbox (badness 1067) in paragraph at lines 2820--2825 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2486] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2487] [2488] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2982--2982 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2489] [2490] [2491] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3178--3178 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2492] Underfull \hbox (badness 10000) in paragraph at lines 3246--3249 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2493] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3296--3296 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3297--3297 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2494] [2495] [2496] Underfull \hbox (badness 10000) in paragraph at lines 3482--3485 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for Underfull \hbox (badness 3471) in paragraph at lines 3482--3485 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2497] Underfull \hbox (badness 10000) in paragraph at lines 3545--3550 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2498] Underfull \hbox (badness 4621) in paragraph at lines 3607--3612 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3607--3612 \T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1 /ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider Underfull \hbox (badness 6268) in paragraph at lines 3619--3622 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2499] [2500] [2501] Underfull \hbox (badness 10000) in paragraph at lines 3804--3807 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3835--3838 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2502] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3888--3888 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3899--3901 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2503] [2504] [2505] [2506] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4092--4092 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4094--4094 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4123--4128 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2507] Underfull \hbox (badness 10000) in paragraph at lines 4190--4198 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2508] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4232--4232 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4241--4241 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4243--4243 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4246--4246 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4248--4248 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4262--4262 [] \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t olerance = 0))[] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2517] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2518] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2519] [2520] [2521]) (./foreign-pkg.tex [2522] Chapter 22. [2523] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2524] [2525] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2526] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2527] [2528] [2529] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2530] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli cated_"\T1/ptm/m/n/10 ) if [2531] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2532] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2534] [2535] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2536] [2537] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2538] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2539] [2540] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2541] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2542] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2543] Underfull \hbox (badness 6725) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by [2544]) (./lattice-pkg.tex Chapter 23. [2545] [2546] [2547] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2548] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2549] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2550] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2551] [2552] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2553] [2554] [2555] [2556] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2557] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2558] [2559] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2560] [2561] [2562] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2563] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2564] Underfull \vbox (badness 10000) has occurred while \output is active [2565] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2566] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2567] Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2568] [2569] [2570] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2571] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2572] [2573] [2574] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2575] [2576] [2577] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2578] [2579] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2580] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2581] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast er[][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2883--2885 []\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T 1/ptm/m/n/10 when [2582] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2583] [2584] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2585] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2586] [2587] [2588] [2589]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2590] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2591] [2592] [2593] [2594] [2595] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2596] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2597] [2598] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4105--4109 \T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se t-tings (ob-tained by [2599] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2600] [2601] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl ot.polygon \T1/ptm/m/n/10 and [2602] [2603] [2604] [2605] [2606] [2607] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2608] [2609] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2610] [2611] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2612] [2613] [2614] [2615] [2616] [2617] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2618] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef t of pan-els us-ing Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2619] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh ich is to draw a strip ap-pro-pri-ate for [2620] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2621] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2622] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2623] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are used (in com-bi-na-tion with [2624] [2625] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2626] [2627] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2628] [2629] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2630] [2631] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2632] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2633] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2634] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2635] [2636] [2637] [2638] [2639] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2640] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2641] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu nc-tion is passed [2642] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2643] [2644] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2645] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2646] [2647] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2648] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2649] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2650] [2651] [2652] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2653] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2662] [2663] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2664] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2665] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2666] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2667] [2668] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2669] [2670] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2671] Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left, right, left.name, right.name, condition Overfull \hbox (104.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name , right.x.name, right.y.name, condition [2672] [2673] [2674] [2675] [2676] [2677] [2678] Underfull \hbox (badness 4205) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2679] [2680] [2681]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2682] [2683] [2684] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes \T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2685] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2686]) (./mgcv-pkg.tex Chapter 24. [2687] [2688] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2689] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2690] [2691] [2692] Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2693] [2694] [2695] [2696] Underfull \hbox (badness 2922) in paragraph at lines 595--596 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2697] [2698] Underfull \hbox (badness 1158) in paragraph at lines 666--668 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2699] Underfull \hbox (badness 1259) in paragraph at lines 729--730 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2700] Underfull \vbox (badness 10000) has occurred while \output is active [2701] [2702] [2703] [2704] [2705] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1078--1078 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1084--1084 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] [2706] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1091--1091 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1093--1093 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",ylim=c(0,1),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2707] [2708] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1231--1231 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2709] [2710] [2711] [2712] [2713] [2714] [2715] [2716] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1686--1686 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2717] [2718] Underfull \vbox (badness 4913) has occurred while \output is active [2719] [2720] [2721] [2722] Underfull \hbox (badness 1052) in paragraph at lines 2061--2069 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2078--2078 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2090--2093 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also [2723] Underfull \hbox (badness 1142) in paragraph at lines 2103--2107 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2129--2134 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2724] [2725] [2726] Underfull \hbox (badness 1043) in paragraph at lines 2294--2300 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2727] [2728] Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2729] Underfull \vbox (badness 10000) has occurred while \output is active [2730] Underfull \vbox (badness 10000) has occurred while \output is active [2731] [2732] [2733] [2734] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2748--2748 [] \T1/pcr/m/n/10 keepData=FALSE,scale.est="fletcher",edge.correct= FALSE)[] [2735] [2736] [2737] [2738] [2739] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3075--3075 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3078--3078 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2740] [2741] [2742] [2743] [2744] [2745] Underfull \hbox (badness 5189) in paragraph at lines 3439--3443 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2746] Underfull \vbox (badness 10000) has occurred while \output is active [2747] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3556--3556 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2748] [2749] Underfull \hbox (badness 1184) in paragraph at lines 3725--3729 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4171--4171 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2758] [2759] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4321--4321 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2760] [2761] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4415--4415 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] Underfull \hbox (badness 1142) in paragraph at lines 4446--4450 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2762] Underfull \hbox (badness 10000) in paragraph at lines 4515--4524 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2763] [2764] Underfull \hbox (badness 5970) in paragraph at lines 4632--4638 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4632--4638 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2765] Underfull \vbox (badness 10000) has occurred while \output is active [2766] [2767] [2768] Underfull \hbox (badness 1577) in paragraph at lines 4912--4915 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 4919--4920 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2769] [2770] [2771] [2772] [2773] [2774] [2775] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5314--5314 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2776] [2777] [2778] [2779] [2780] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5638--5638 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2781] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5640--5640 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5661--5665 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2782] [2783] [2784] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5797--5797 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in i,n.chains=1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5828--5828 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in i,n.chains=1)[] Underfull \vbox (badness 10000) has occurred while \output is active [2785] [2786] Overfull \hbox (72.78088pt too wide) in paragraph at lines 5902--5902 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2787] [2788] [2789] Underfull \vbox (badness 10000) has occurred while \output is active [2790] [2791] [2792] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6281--6281 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [2793] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6308--6308 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2794] [2795] [2796] [2797] [2798] [2799] Underfull \vbox (badness 4366) has occurred while \output is active [2800] [2801] Underfull \hbox (badness 1242) in paragraph at lines 6851--6852 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2802] [2803] [2804] [2805] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7001--7001 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7020--7020 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2806] [2807] [2808] [2809] [2810] [2811] [2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] Underfull \vbox (badness 10000) has occurred while \output is active [2824] [2825] Underfull \hbox (badness 10000) in paragraph at lines 8240--8243 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8240--8243 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8240--8243 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2826] Underfull \hbox (badness 10000) in paragraph at lines 8296--8299 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8296--8299 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2827] [2828] [2829] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8516--8516 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8517--8517 [] \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla b=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8520--8520 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2830] [2831] [2832] Underfull \hbox (badness 1629) in paragraph at lines 8675--8680 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2833] [2834] [2835] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8876--8876 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2836] [2837] [2838] [2839] [2840] [2841] Underfull \vbox (badness 10000) has occurred while \output is active [2842] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9304--9304 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2843] Underfull \hbox (badness 1205) in paragraph at lines 9342--9344 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9342--9344 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9348--9353 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2844] Underfull \hbox (badness 1205) in paragraph at lines 9432--9434 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9432--9434 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2845] Underfull \hbox (badness 10000) in paragraph at lines 9501--9504 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9501--9504 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2846] [2847] [2848] Underfull \hbox (badness 1253) in paragraph at lines 9631--9633 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2849] [2850] Underfull \vbox (badness 10000) has occurred while \output is active [2851] Underfull \hbox (badness 1946) in paragraph at lines 9809--9816 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 9809--9816 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 9809--9816 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 9817--9820 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 9817--9820 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2852] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9883--9883 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] [2853] Underfull \hbox (badness 10000) in paragraph at lines 9912--9915 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2854] [2855] [2856] [2857] [2858] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10199--10199 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2859] [2860] [2861] [2862] [2863] Underfull \vbox (badness 10000) has occurred while \output is active [2864] Underfull \hbox (badness 3861) in paragraph at lines 10540--10543 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10547--10547 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10560--10564 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2865] Underfull \hbox (badness 10000) in paragraph at lines 10600--10604 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2866] [2867] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10741--10741 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 10752--10757 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2868] [2869] Underfull \hbox (badness 1803) in paragraph at lines 10829--10833 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 10841--10853 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 10858--10862 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 10858--10862 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2870] [2871] [2872] Underfull \hbox (badness 6876) in paragraph at lines 11053--11059 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like [2873] Underfull \hbox (badness 10000) in paragraph at lines 11094--11095 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2874] [2875] Underfull \hbox (badness 10000) in paragraph at lines 11212--11213 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2876] [2877] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11277--11277 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11288--11288 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11289--11289 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11294--11294 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11300--11300 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11301--11301 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] Underfull \vbox (badness 10000) has occurred while \output is active [2878] Underfull \hbox (badness 10000) in paragraph at lines 11370--11372 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11370--11372 \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs", ...) \T1/ptm/m/n/10 or [2879] [2880] Underfull \hbox (badness 10000) in paragraph at lines 11498--11499 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2881] [2882] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11579--11579 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11580--11580 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2883] Underfull \hbox (badness 7613) in paragraph at lines 11618--11621 \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p tm/m/n/10 pro-duced by the [2884] [2885] Underfull \hbox (badness 10000) in paragraph at lines 11727--11728 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2886] [2887] [2888] [2889] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11964--11964 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] Underfull \hbox (badness 10000) in paragraph at lines 12009--12011 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2890] [2891] Underfull \vbox (badness 10000) has occurred while \output is active [2892] Underfull \hbox (badness 10000) in paragraph at lines 12168--12171 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12168--12171 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12168--12171 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2893] [2894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12250--12250 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12295--12301 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12295--12301 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2895] [2896] [2897] Underfull \vbox (badness 10000) has occurred while \output is active [2898] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12509--12509 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2899] [2900] Underfull \hbox (badness 10000) in paragraph at lines 12612--12620 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 12638--12639 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2901] [2902] [2903] [2904] Underfull \hbox (badness 3396) in paragraph at lines 12899--12902 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2905] Underfull \hbox (badness 10000) in paragraph at lines 12944--12946 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2906] [2907] [2908] [2909] Underfull \hbox (badness 10000) in paragraph at lines 13168--13171 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13168--13171 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [2910] Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [2911] [2912] [2913] [2914] Underfull \hbox (badness 2158) in paragraph at lines 13442--13442 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2915] Overfull \hbox (48.78088pt too wide) in paragraph at lines 13517--13517 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2916] [2917] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13651--13651 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2918] [2919] Underfull \hbox (badness 4846) in paragraph at lines 13779--13782 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [2920] [2921] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] [2931] [2932] [2933] Underfull \hbox (badness 10000) in paragraph at lines 14604--14612 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 14604--14612 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2934] [2935] [2936] [2937] Overfull \hbox (24.78088pt too wide) in paragraph at lines 14876--14876 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2938] [2939] [2940] [2941] [2942] [2943] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15170--15170 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15171--15171 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15183--15183 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2944] [2945] [2946]) (./nlme-pkg.tex Chapter 25. [2947] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2948] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2949] [2950] [2951] [2952] [2953] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2954] [2955] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [2964] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [2965] [2966] [2967] [2968] [2969] [2970] [2971] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [2972] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [2973] [2974] [2975] [2976] [2977] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [2978] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [2979] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [2980] [2981] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [2982] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001] [3002] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3003] [3004] [3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3027] [3028] [3029] [3030] [3031] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3032] [3033] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041] [3042] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3043] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3044] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3045] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3046] [3047] [3048] [3049] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3050] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , [3051] Underfull \hbox (badness 10000) in paragraph at lines 6717--6719 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3052] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6747--6747 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3053] [3054] [3055] Underfull \hbox (badness 10000) in paragraph at lines 6990--6997 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3056] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7007--7007 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7015--7015 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7037--7039 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3057] [3058] [3059] Underfull \hbox (badness 10000) in paragraph at lines 7252--7257 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3060] [3061] [3062] Underfull \hbox (badness 10000) in paragraph at lines 7404--7412 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7404--7412 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 1817) in paragraph at lines 7404--7412 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7427--7430 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3063] [3064] [3065] Underfull \hbox (badness 3354) in paragraph at lines 7642--7644 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3066] [3067] [3068] [3069] [3070] [3071] Underfull \hbox (badness 1642) in paragraph at lines 8034--8056 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3072] [3073] Underfull \hbox (badness 10000) in paragraph at lines 8154--8171 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8154--8171 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8197--8197 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8206--8228 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3074] [3075] [3076] [3077] [3078] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8471--8471 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8516--8518 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3079] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8554--8554 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8561 \aliasA{sigma}{lmeObject}{sigma} [3080] [3081] [3082] Underfull \hbox (badness 10000) in paragraph at lines 8722--8734 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] Underfull \hbox (badness 10000) in paragraph at lines 9313--9320 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9324--9324 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3092] Underfull \hbox (badness 6300) in paragraph at lines 9406--9409 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3093] [3094] [3095] [3096]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3097] Underfull \hbox (badness 10000) in paragraph at lines 9695--9698 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9739--9742 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9739--9742 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3098] [3099] [3100] Underfull \hbox (badness 2435) in paragraph at lines 9913--9918 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3101] [3102] [3103] [3104] [3105] Underfull \hbox (badness 7291) in paragraph at lines 10203--10205 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3106] [3107] [3108] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10419--10419 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3109] Underfull \hbox (badness 1596) in paragraph at lines 10448--10474 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3110] [3111] [3112] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10624--10624 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3113] [3114] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10775--10775 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] [3115] Underfull \hbox (badness 10000) in paragraph at lines 10821--10823 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Underfull \hbox (badness 1092) in paragraph at lines 10833--10836 []\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr /m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used Overfull \hbox (9.78043pt too wide) in paragraph at lines 10856--10856 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3116] [3117] [3118] [3119] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11112--11112 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] Underfull \hbox (badness 6268) in paragraph at lines 11891--11901 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3132] [3133] [3134] [3135] Underfull \hbox (badness 10000) in paragraph at lines 12152--12158 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3136] [3137] [3138] [3139] [3140] Underfull \hbox (badness 6876) in paragraph at lines 12474--12476 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3141] [3142] Underfull \hbox (badness 2452) in paragraph at lines 12630--12637 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3143] Underfull \hbox (badness 10000) in paragraph at lines 12695--12701 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13647--13647 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3158] Underfull \hbox (badness 10000) in paragraph at lines 13674--13677 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 6016) in paragraph at lines 13702--13705 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13702--13705 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13709--13712 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13717--13724 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13717--13724 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner [3159] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13774--13774 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13781--13784 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13781--13784 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle [3160] Underfull \hbox (badness 4582) in paragraph at lines 13809--13812 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13809--13812 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13813--13816 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3161] Underfull \hbox (badness 10000) in paragraph at lines 13889--13892 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 1472) in paragraph at lines 13914--13921 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3162] Underfull \hbox (badness 10000) in paragraph at lines 13983--13985 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3163] [3164] [3165] [3166] Underfull \hbox (badness 1540) in paragraph at lines 14198--14203 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14245--14247 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3167] [3168] [3169] [3170] [3171] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14489--14489 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15142 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15142 ...Extract Random Effects}{random.effects} [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] Underfull \hbox (badness 1009) in paragraph at lines 15799--15808 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3191] [3192] [3193] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15946--15946 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3194] [3195] [3196] [3197] Underfull \hbox (badness 10000) in paragraph at lines 16224--16242 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16224--16242 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3198] Underfull \hbox (badness 10000) in paragraph at lines 16281--16287 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3199] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16312--16312 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3200] [3201] [3202] [3203] [3204] [3205] [3206] Underfull \hbox (badness 1728) in paragraph at lines 16801--16804 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3207] [3208] [3209] [3210] [3211] Underfull \hbox (badness 1867) in paragraph at lines 17136--17145 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3212] Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , [3213] [3214] [3215] [3216] Underfull \hbox (badness 10000) in paragraph at lines 17447--17454 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 10000) in paragraph at lines 17977--17987 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17977--17987 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18015--18020 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3225] Underfull \hbox (badness 3579) in paragraph at lines 18079--18084 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3226] Underfull \hbox (badness 3579) in paragraph at lines 18142--18147 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3227] Underfull \hbox (badness 1577) in paragraph at lines 18203--18205 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18205--18210 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3228] Underfull \hbox (badness 3579) in paragraph at lines 18268--18273 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3229] Underfull \hbox (badness 10000) in paragraph at lines 18301--18310 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18301--18310 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18340--18345 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3230] [3231] [3232] Underfull \hbox (badness 1009) in paragraph at lines 18489--18498 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3233] [3234] Underfull \hbox (badness 1009) in paragraph at lines 18623--18632 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3243] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3244] [3245] [3246] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3247] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3248] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3249] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3250]) (./rpart-pkg.tex Chapter 27. [3251] [3252] [3253] [3254] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3255] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3256] [3257] [3258] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3259] [3260] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3261] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3262] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3263] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3264] [3265] [3266] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3267] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3268] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3269] [3270] [3271] [3272] [3273] [3274] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3275] [3276] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3277] [3278] [3279]) (./spatial-pkg.tex [3280] Chapter 28. [3281] [3282] [3283] [3284] [3285] [3286] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3287] [3288] [3289] [3290] [3291] [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299]) (./survival-pkg.tex [3300] Chapter 29. [3301] [3302] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3303] [3304] Overfull \hbox (42.78088pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho d, rownames) Overfull \hbox (42.78088pt too wide) in paragraph at lines 279--279 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho d, rownames)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.319 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.319 ... Myelogenous Leukemia survival data}{aml} [3305] [3306] Overfull \hbox (9.78043pt too wide) in paragraph at lines 416--416 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 418--418 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3307] Overfull \hbox (6.78088pt too wide) in paragraph at lines 455--455 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3308] [3309] Underfull \vbox (badness 10000) has occurred while \output is active [3310] Overfull \hbox (36.78088pt too wide) in paragraph at lines 654--654 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 655--655 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3311] [3312] Overfull \hbox (9.78043pt too wide) in paragraph at lines 798--798 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3313] [3314] [3315] Underfull \hbox (badness 1097) in paragraph at lines 968--970 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 988--988 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3316] [3317] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1103--1103 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3318]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1171 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3319] [3320] [3321] [3322] [3323] [3324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1623--1623 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3325] [3326] [3327] [3328] [3329] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1988--1988 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3330] [3331] [3332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2237--2237 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3333] [3334] [3335] [3336] [3337] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2554--2554 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Underfull \hbox (badness 1389) in paragraph at lines 2567--2569 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3338] Underfull \hbox (badness 1048) in paragraph at lines 2621--2623 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3339] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2698--2698 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] [3340] [3341] [3342] [3343] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2945--2945 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3344] [3345] [3346] [3347] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3211--3211 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3348] [3349] [3350] [3351] Underfull \vbox (badness 10000) has occurred while \output is active [3352] [3353] [3354] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3620--3620 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc ale=1,[] [3355] [3356] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3809--3809 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3357] [3358] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3925--3925 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3359] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4015--4015 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3360] [3361] [3362] Underfull \hbox (badness 1852) in paragraph at lines 4163--4165 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3363] [3364] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4297--4297 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4298--4298 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3365] [3366] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4462--4462 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3367] Underfull \hbox (badness 1540) in paragraph at lines 4517--4520 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4564--4564 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3368] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4585--4585 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3369] [3370] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4732--4732 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] [3371] Underfull \vbox (badness 10000) has occurred while \output is active [3372] [3373] [3374] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5017--5017 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response" \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 \T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n /10 . See the La-TeX doc-u-men-ta-tion [3375] [3376] [3377] [3378] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5302--5302 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5303--5303 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] [3379] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5358--5358 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3380] [3381] [3382] [3383] [3384] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5693--5693 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5694--5694 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3385] [3386] [3387] [3388] Overfull \hbox (54.78088pt too wide) in paragraph at lines 5995--5995 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3389] [3390] [3391] [3392] Underfull \hbox (badness 10000) in paragraph at lines 6255--6264 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3393] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6365--6365 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] [3394] Underfull \hbox (badness 1038) in paragraph at lines 6407--6413 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival Underfull \hbox (badness 3000) in paragraph at lines 6429--6431 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, [3395] Overfull \hbox (48.78088pt too wide) in paragraph at lines 6459--6459 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3396] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6545--6545 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3397] [3398] [3399] Underfull \hbox (badness 10000) in paragraph at lines 6770--6775 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , Overfull \hbox (18.78088pt too wide) in paragraph at lines 6791--6791 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T RUE, id,[] [3400] [3401] [3402] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7007--7007 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3403] Underfull \hbox (badness 6332) in paragraph at lines 7114--7119 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3404] [3405] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7294--7294 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3406] [3407] [3408] [3409] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3410] Underfull \hbox (badness 1354) in paragraph at lines 7622--7626 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3411] [3412] Underfull \hbox (badness 2035) in paragraph at lines 7798--7805 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 7798--7805 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 7798--7805 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3413] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7874--7874 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3414] [3415] [3416] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8032--8032 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3417] [3418] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8164--8164 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8167--8167 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3419] [3420] [3421] [3422] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8464--8464 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8465--8465 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8471--8471 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8473--8473 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3423] [3424] [3425] [3426] Underfull \vbox (badness 10000) has occurred while \output is active [3427] [3428]) No file fullrefman.ind. 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [20-Nov-2007] (kpathsea + Thai support). Scanning input file fullrefman.idx...........................done (23506 entries accepted, 76 rejected). Sorting entries..........................................................................................................................................................................................................................................................................done (394087 comparisons). Generating output file fullrefman.ind.........................done (19130 lines written, 111 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./fullrefman.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. 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Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 366. ) (/usr/share/texmf-texlive/tex/latex/base/inputenc.sty (/usr/share/texmf-texlive/tex/latex/base/utf8.def (/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu))) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg))) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) Writing index file fullrefman.idx (./fullrefman.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./fullrefman.out) (./fullrefman.out) (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd) [1{/var/c ache/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc (/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]) [49] [50] [1] [2] (./base-pkg.tex Chapter 1. Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m /n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 338--341 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] Underfull \hbox (badness 2359) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 533--539 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15] Overfull \hbox (0.78088pt too wide) in paragraph at lines 857--857 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20] [21] [22] [23] Underfull \hbox (badness 5862) in paragraph at lines 1378--1384 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1632--1632 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1648--1654 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of [27] Underfull \hbox (badness 1303) in paragraph at lines 1658--1661 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 2865) in paragraph at lines 1760--1764 []\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/ m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then Underfull \hbox (badness 10000) in paragraph at lines 1764--1766 []\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1901--1901 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1936--1938 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1939--1941 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2193--2193 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [35] [36] Underfull \hbox (badness 1107) in paragraph at lines 2326--2328 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [37] [38] [39] [40] [41] Underfull \hbox (badness 5878) in paragraph at lines 2658--2663 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2658--2663 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [57] [58] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3848--3848 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [59] [60] [61] [62] Underfull \hbox (badness 4927) in paragraph at lines 4071--4075 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4071--4075 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [63] [64] Underfull \hbox (badness 4595) in paragraph at lines 4215--4218 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [65] [66] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Underfull \hbox (badness 1199) in paragraph at lines 4400--4406 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- [67] Underfull \hbox (badness 2573) in paragraph at lines 4411--4414 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [68] Underfull \hbox (badness 10000) in paragraph at lines 4491--4496 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4491--4496 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4491--4496 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [69] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4570--4570 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [70] [71] [72] [73] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [74] [75] [76] [77] [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 5212--5220 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [80] [81] [82] [83] [84] [85] [86] [87] Underfull \hbox (badness 1796) in paragraph at lines 5758--5766 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [88] [89] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5952--5952 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 5954--5954 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5955--5955 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [90] [91] Underfull \hbox (badness 1635) in paragraph at lines 6116--6119 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class [92] Underfull \hbox (badness 3009) in paragraph at lines 6120--6123 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing Underfull \hbox (badness 1102) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6151--6159 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [93] [94] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6299--6299 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [95] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6341--6343 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [96] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6483--6486 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [97] [98] [99] Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6666--6668 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 1067) in paragraph at lines 6708--6715 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [100] [101] Underfull \vbox (badness 10000) has occurred while \output is active [102] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6894--6894 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [103] [104] Underfull \hbox (badness 1231) in paragraph at lines 7019--7025 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [105] [106] [107] Underfull \hbox (badness 10000) in paragraph at lines 7230--7232 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [108] [109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7375--7375 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [110] Underfull \hbox (badness 4595) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [111] [112] [113] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [114] [115] Underfull \hbox (badness 8132) in paragraph at lines 7714--7718 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7714--7718 \T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , but this can be changed by set-ting Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1062) in paragraph at lines 7733--7743 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be Overfull \hbox (4.63962pt too wide) in paragraph at lines 7765--7769 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [116] Underfull \hbox (badness 7451) in paragraph at lines 7804--7814 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7804--7814 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [117] [118] [119] [120] [121] Underfull \hbox (badness 10000) in paragraph at lines 8211--8223 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8211--8223 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [122] [123] [124] Underfull \hbox (badness 5802) in paragraph at lines 8420--8424 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a [125] [126] [127] Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [128] [129] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8728--8728 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8730--8730 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [130] [131] Underfull \hbox (badness 4254) in paragraph at lines 8891--8895 []\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so urce \T1/ptm/m/n/10 at-tribute), use [132] Underfull \hbox (badness 1132) in paragraph at lines 8951--8958 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [133] Underfull \hbox (badness 1603) in paragraph at lines 9064--9067 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1917) in paragraph at lines 9664--9669 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [143] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9719--9719 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9720--9720 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [144] Underfull \hbox (badness 1168) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [145] [146] Underfull \hbox (badness 2828) in paragraph at lines 9960--9964 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 9960--9964 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ [147] [148] [149] [150] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10201--10201 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [151] Underfull \hbox (badness 1629) in paragraph at lines 10275--10279 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [152] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [153] Underfull \hbox (badness 3690) in paragraph at lines 10389--10397 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10398--10400 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than Underfull \hbox (badness 3735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [154] [155] [156] Underfull \hbox (badness 10000) in paragraph at lines 10624--10627 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [157] [158] [159] [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 5288) in paragraph at lines 11306--11308 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11316--11321 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [166] Underfull \hbox (badness 10000) in paragraph at lines 11376--11378 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [167] [168] Underfull \hbox (badness 4569) in paragraph at lines 11493--11497 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11493--11497 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [169] [170] Underfull \hbox (badness 10000) in paragraph at lines 11608--11610 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as Underfull \hbox (badness 2790) in paragraph at lines 11651--11653 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [171] [172] [173] Underfull \hbox (badness 4048) in paragraph at lines 11822--11832 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 11822--11832 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [174] [175] [176] Underfull \hbox (badness 5460) in paragraph at lines 12070--12079 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [177] [178] [179] [180] [181] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12444--12444 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [182] [183] [184] [185] Underfull \hbox (badness 5119) in paragraph at lines 12729--12732 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [186] [187] Underfull \hbox (badness 2221) in paragraph at lines 12889--12898 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s [188] [189] [190] [191] Underfull \hbox (badness 2253) in paragraph at lines 13141--13143 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 13256--13258 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 13406--13408 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 13514--13518 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13525--13528 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . [198] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13566--13566 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [199] Underfull \hbox (badness 10000) in paragraph at lines 13658--13661 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13668--13668 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [200] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13756--13756 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, [201] Underfull \hbox (badness 7238) in paragraph at lines 13780--13787 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13780--13787 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 13780--13787 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- Underfull \hbox (badness 3965) in paragraph at lines 13788--13792 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [202] [203] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13951--13951 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 13952--13952 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 14031--14035 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14031--14035 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [206] [207] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14179--14179 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14182--14182 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [208] Underfull \hbox (badness 1168) in paragraph at lines 14266--14270 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14266--14270 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [209] Underfull \hbox (badness 6944) in paragraph at lines 14361--14364 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [210] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14386--14386 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 14520--14522 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14539--14539 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14541--14541 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14544--14544 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14550--14553 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 4254) in paragraph at lines 14566--14574 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14581--14585 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [213] Underfull \hbox (badness 10000) in paragraph at lines 14650--14652 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so [214] Underfull \hbox (badness 10000) in paragraph at lines 14656--14660 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, Underfull \hbox (badness 10000) in paragraph at lines 14656--14660 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14661--14669 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or Underfull \hbox (badness 3601) in paragraph at lines 14695--14699 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 14695--14699 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [215] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14762--14762 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [216] Overfull \hbox (25.98041pt too wide) in paragraph at lines 14784--14784 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2418) in paragraph at lines 15705--15709 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 15712--15715 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 15740--15747 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [230] [231] [232] [233] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15986--15986 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16011--16018 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [234] [235] [236] [237] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16279--16279 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16308--16308 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [238] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16359--16359 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16365--16369 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16365--16369 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [239] [240] [241] [242] [243] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16718--16718 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [244] [245] [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16968--16968 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [247] [248] [249] [250] Underfull \hbox (badness 2435) in paragraph at lines 17229--17231 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [251] Underfull \hbox (badness 1867) in paragraph at lines 17271--17278 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17271--17278 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17271--17278 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17286--17288 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17294--17294 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17304--17304 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [252] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17324--17324 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [253] [254] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17458--17458 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17464--17464 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17467--17467 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17473--17473 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [255] [256] [257] [258] [259] Underfull \hbox (badness 10000) in paragraph at lines 17812--17814 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [260] Underfull \hbox (badness 4217) in paragraph at lines 17896--17905 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 17911--17927 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 4699) in paragraph at lines 18325--18328 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [267] [268] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18448--18448 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [269] [270] Underfull \hbox (badness 4739) in paragraph at lines 18583--18585 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [271] [272] [273] [274] [275] [276] [277] Underfull \hbox (badness 1430) in paragraph at lines 18996--19001 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 18996--19001 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [278] Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19057--19062 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [279] Underfull \hbox (badness 10000) in paragraph at lines 19117--19124 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19117--19124 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19117--19124 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19117--19124 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19133--19135 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [280] Underfull \hbox (badness 1975) in paragraph at lines 19205--19208 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [281] [282] [283] [284] [285] [286] Underfull \hbox (badness 1077) in paragraph at lines 19600--19605 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [287] Underfull \hbox (badness 10000) in paragraph at lines 19614--19621 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [288] Underfull \hbox (badness 10000) in paragraph at lines 19688--19692 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [289] Underfull \hbox (badness 10000) in paragraph at lines 19818--19822 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 19818--19822 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self [290] [291] Underfull \hbox (badness 10000) in paragraph at lines 19916--19923 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [292] [293] Underfull \hbox (badness 10000) in paragraph at lines 20037--20041 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [294] Underfull \hbox (badness 5161) in paragraph at lines 20092--20097 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [295] [296] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20259--20259 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20263--20263 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [297] Underfull \hbox (badness 3343) in paragraph at lines 20319--20323 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [298] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20405--20405 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20416--20416 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [299] [300] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20525--20525 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (85.38034pt too wide) in paragraph at lines 20528--20528 []\T1/pcr/m/n/9 attach("all.RData") # safer and will warn about masked objects w/ same name in .GlobalEnv[] [301] Underfull \hbox (badness 6380) in paragraph at lines 20572--20577 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20630--20637 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20630--20637 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20630--20637 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [302] Underfull \hbox (badness 2564) in paragraph at lines 20650--20653 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 20680--20680 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [303] Underfull \hbox (badness 1205) in paragraph at lines 20703--20708 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [304] [305] [306] [307] Underfull \hbox (badness 2469) in paragraph at lines 21013--21019 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 1939) in paragraph at lines 21013--21019 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing names. Underfull \hbox (badness 10000) in paragraph at lines 21013--21019 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [308] [309] [310] [311] Underfull \hbox (badness 10000) in paragraph at lines 21327--21329 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [312] [313] [314] [315] [316] Overfull \hbox (52.98038pt too wide) in paragraph at lines 21631--21631 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 21632--21632 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21635--21635 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [317] [318] Underfull \hbox (badness 1655) in paragraph at lines 21759--21763 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [319] [320] [321] [322] Underfull \hbox (badness 2277) in paragraph at lines 22008--22011 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [323] [324] [325] [326] [327] [328] [329] Underfull \hbox (badness 10000) in paragraph at lines 22491--22497 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22491--22497 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins [330] Underfull \hbox (badness 1484) in paragraph at lines 22523--22531 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 2951) in paragraph at lines 22523--22531 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22523--22531 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [331] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22600--22600 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [332] Underfull \hbox (badness 10000) in paragraph at lines 22651--22655 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 22651--22655 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 10000) in paragraph at lines 23091--23099 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; [339] Underfull \hbox (badness 3849) in paragraph at lines 23205--23210 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [340] Underfull \hbox (badness 7308) in paragraph at lines 23282--23288 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5077) in paragraph at lines 23282--23288 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23292--23295 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23292--23295 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [341] [342] [343] Underfull \hbox (badness 10000) in paragraph at lines 23444--23446 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] Underfull \hbox (badness 2197) in paragraph at lines 24122--24126 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24122--24126 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24136--24140 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24136--24140 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to [354] Underfull \hbox (badness 10000) in paragraph at lines 24229--24235 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 24229--24235 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 24242--24244 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [355] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24293--24293 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [356] [357] [358] Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [359] Underfull \hbox (badness 4120) in paragraph at lines 24572--24579 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [360] [361] Underfull \hbox (badness 1694) in paragraph at lines 24708--24711 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [362] [363] [364] [365] Underfull \hbox (badness 1603) in paragraph at lines 24947--24949 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [366] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25065--25073 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [367] [368] Underfull \hbox (badness 5475) in paragraph at lines 25202--25212 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25244--25247 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25259--25261 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [369] [370] [371] Underfull \hbox (badness 3138) in paragraph at lines 25518--25524 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25518--25524 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 25518--25524 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 25531--25534 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 25555--25557 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25567--25571 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25567--25571 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is [372] Underfull \hbox (badness 10000) in paragraph at lines 25572--25578 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 25587--25592 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 25593--25604 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 25605--25608 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25615--25627 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 25615--25627 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a Underfull \hbox (badness 10000) in paragraph at lines 25629--25636 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25629--25636 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25629--25636 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 25629--25636 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [373] [374] [375] [376] [377] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25963--25963 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 25976--25980 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25976--25980 \T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.y)] [378] [379] [380] [381] [382] Underfull \hbox (badness 4341) in paragraph at lines 26299--26301 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26335--26341 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*, collapse=", ")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with [383] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26357--26357 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26369--26369 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [384] [385] [386] [387] [388] [389] [390] Underfull \hbox (badness 10000) in paragraph at lines 26802--26806 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [391] Underfull \hbox (badness 1796) in paragraph at lines 26865--26868 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 27060--27063 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [395] [396] [397] [398] [399] [400] [401] [402] [403] Underfull \hbox (badness 1226) in paragraph at lines 27692--27697 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [404] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27737--27737 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [405] [406] [407] [408] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28003--28003 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28014--28014 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28020--28020 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28021--28021 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28024--28024 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [409] Underfull \hbox (badness 7415) in paragraph at lines 28099--28103 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [410] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28120--28120 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [411] Underfull \hbox (badness 2418) in paragraph at lines 28268--28279 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [412] [413] Underfull \hbox (badness 1248) in paragraph at lines 28392--28399 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 28392--28399 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [414] Underfull \hbox (badness 1533) in paragraph at lines 28501--28504 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [415] [416] Underfull \hbox (badness 1337) in paragraph at lines 28598--28601 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [417] Overfull \hbox (42.78088pt too wide) in paragraph at lines 28646--28646 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 28663--28674 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in Underfull \hbox (badness 10000) in paragraph at lines 28675--28678 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [418] [419] Underfull \hbox (badness 1117) in paragraph at lines 28770--28776 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [420] [421] [422] [423] [424] [425] Underfull \hbox (badness 4048) in paragraph at lines 29148--29153 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29148--29153 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29148--29153 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [426] [427] [428] [429] [430] [431] [432] [433] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29686--29686 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [434] [435] [436] [437] Overfull \hbox (13.9408pt too wide) in paragraph at lines 29970--29972 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [438] [439] Underfull \hbox (badness 7558) in paragraph at lines 30186--30190 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 30196--30198 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the [440] Underfull \hbox (badness 5417) in paragraph at lines 30201--30204 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30205--30207 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30208--30210 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 10000) in paragraph at lines 30615--30619 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31300--31300 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 31431--31435 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31431--31435 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [459] [460] [461] Underfull \hbox (badness 2302) in paragraph at lines 31671--31678 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [462] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31723--31723 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [463] Underfull \hbox (badness 1158) in paragraph at lines 31827--31832 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [464] Underfull \hbox (badness 10000) in paragraph at lines 31854--31860 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 31854--31860 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [465] Underfull \hbox (badness 10000) in paragraph at lines 31930--31935 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 31930--31935 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [466] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32012--32012 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [467] [468] [469] Underfull \hbox (badness 2809) in paragraph at lines 32276--32282 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32283--32286 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1735) in paragraph at lines 33087--33093 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [482] Underfull \hbox (badness 4303) in paragraph at lines 33103--33106 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [483] [484] [485] [486] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33421--33421 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [487] [488] [489] [490] Overfull \hbox (6.78088pt too wide) in paragraph at lines 33670--33670 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 33672--33672 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 10000) in paragraph at lines 33715--33721 [][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/ m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/ 10 , see Underfull \hbox (badness 10000) in paragraph at lines 33715--33721 \T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T 1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard- Underfull \hbox (badness 10000) in paragraph at lines 33715--33721 \T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i s the de-fault cur-rently; [491] Underfull \hbox (badness 2512) in paragraph at lines 33730--33732 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [492] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33826--33826 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:[] [493] [494] [495] [496] [497] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34154--34154 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34169--34169 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [498] [499] [500] [501] [502] [503] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34608--34608 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 34609--34609 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [504] [505] [506] [507] Overfull \hbox (63.78036pt too wide) in paragraph at lines 34873--34873 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [508] Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 34957--34967 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [509] Underfull \hbox (badness 10000) in paragraph at lines 35001--35007 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35001--35007 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 35001--35007 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35013--35020 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35013--35020 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35013--35020 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [510] [511] [512] [513] [514] Underfull \hbox (badness 10000) in paragraph at lines 35311--35317 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [515] [516] Underfull \hbox (badness 1163) in paragraph at lines 35499--35506 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 35499--35506 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [517] [518] [519] [520] Underfull \hbox (badness 1142) in paragraph at lines 35762--35768 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 35777--35777 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [521] [522] [523] [524] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36025--36025 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [525] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36069--36069 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [526] [527] [528] [529] [530] [531] Overfull \hbox (52.98038pt too wide) in paragraph at lines 36501--36501 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 36504--36504 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [532] Underfull \hbox (badness 10000) in paragraph at lines 36555--36562 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 36555--36562 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [533] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36606--36606 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [534] [535] [536] Underfull \hbox (badness 2762) in paragraph at lines 36841--36850 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 36841--36850 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [537] Overfull \hbox (31.3804pt too wide) in paragraph at lines 36903--36903 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [538] Underfull \vbox (badness 7777) has occurred while \output is active [539] [540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37068--37068 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [541] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37106--37106 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 3219) in paragraph at lines 37155--37160 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37155--37160 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [542] Underfull \hbox (badness 2452) in paragraph at lines 37245--37248 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37245--37248 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 37432--37436 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 37447--37450 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [546] [547] [548] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37640--37640 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [549] [550] [551] Underfull \hbox (badness 1082) in paragraph at lines 37778--37781 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [552] [553] Underfull \hbox (badness 1038) in paragraph at lines 37965--37968 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [554] [555] [556] [557] [558] Underfull \hbox (badness 1515) in paragraph at lines 38304--38307 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [559] [560] [561] Underfull \hbox (badness 4096) in paragraph at lines 38529--38532 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 38643--38647 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [564] [565] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38794--38794 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 38796--38796 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 38798--38798 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] [566] Underfull \hbox (badness 10000) in paragraph at lines 38811--38813 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [567] Underfull \hbox (badness 10000) in paragraph at lines 38891--38894 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [568] [569] Underfull \hbox (badness 1867) in paragraph at lines 39009--39013 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39071--39075 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1371) in paragraph at lines 39431--39435 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 TZ \T1/ptm/m/n/10 is set but empty or in-val id, most plat-forms de-fault to `\T1/pcr/m/n/10 UTC\T1/ptm/m/n/10 ', the time z one col- Underfull \hbox (badness 1648) in paragraph at lines 39431--39435 \T1/ptm/m/n/10 lo-qui-ally known as `\T1/pcr/m/n/10 GMT\T1/ptm/m/n/10 ' (see [] []$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Coordinated _ [576] Underfull \hbox (badness 5637) in paragraph at lines 39504--39513 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the Ol-son/IANA Underfull \hbox (badness 1629) in paragraph at lines 39504--39513 \T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion in the file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 39514--39521 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 39514--39521 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 39514--39521 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [577] [578] [579] [580] Underfull \hbox (badness 10000) in paragraph at lines 39798--39800 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [581] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39920--39920 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39922--39922 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [582] [583] [584] [585] [586] Underfull \hbox (badness 6542) in paragraph at lines 40258--40260 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [587] [588] [589] Underfull \hbox (badness 3460) in paragraph at lines 40424--40427 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 40431--40439 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 40431--40439 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less Underfull \hbox (badness 10000) in paragraph at lines 40440--40444 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 40440--40444 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 40440--40444 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 40461--40466 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [590] Underfull \hbox (badness 3895) in paragraph at lines 40523--40535 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 40523--40535 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [591] [592] [593] Underfull \hbox (badness 10000) in paragraph at lines 40708--40711 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [594] [595] Overfull \hbox (9.78043pt too wide) in paragraph at lines 40845--40845 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [596] [597] [598] [599] [600] [601] [602] Underfull \hbox (badness 1803) in paragraph at lines 41396--41399 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), [603] Underfull \hbox (badness 2334) in paragraph at lines 41400--41407 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 4726) in paragraph at lines 41426--41430 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 41426--41430 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [604] [605] [606] Underfull \hbox (badness 3668) in paragraph at lines 41615--41617 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [607] [608] [609] [610] Underfull \hbox (badness 6220) in paragraph at lines 41897--41902 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 41897--41902 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 41897--41902 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 41913--41918 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 1603) in paragraph at lines 41932--41936 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [611] Underfull \hbox (badness 10000) in paragraph at lines 41997--42000 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 41997--42000 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42003--42009 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and [612] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42038--42038 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [613] Underfull \hbox (badness 1622) in paragraph at lines 42116--42118 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [614] [615] [616] [617] Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [618] Underfull \hbox (badness 2846) in paragraph at lines 42470--42474 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42510--42510 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 42531--42535 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [620]) (./compiler-pkg.tex Chapter 2. [621] [622] [623] [624]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [625] [626] [627] [628] [629] Overfull \hbox (15.18042pt too wide) in paragraph at lines 294--294 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [630] Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [631] [632] [633] [634] [635] Overfull \hbox (66.81013pt too wide) in paragraph at lines 691--694 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [636] [637] Overfull \hbox (66.81013pt too wide) in paragraph at lines 824--827 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [638] [639] [640] [641] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [642] [643] [644] [645] [646] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 1525--1528 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1525--1528 \T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m /n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a bove [649] Underfull \hbox (badness 1325) in paragraph at lines 1606--1611 []\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [650] [651] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1713--1716 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [652] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1815--1815 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [653] [654] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1931--1931 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1932--1932 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [655] [656] [657] [658] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2135--2138 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [659] [660] [661] [662] [663] [664] [665] [666] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2676--2679 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [667] Overfull \vbox (13.87083pt too high) has occurred while \output is active [668] Underfull \vbox (badness 1789) has occurred while \output is active [669] [670] Overfull \vbox (12.25539pt too high) has occurred while \output is active [671] [672] Overfull \vbox (17.12102pt too high) has occurred while \output is active [673] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3105--3105 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [674] [675] [676] [677] [678] [679] [680] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3562--3562 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [681] [682] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3710--3713 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [683] Overfull \vbox (10.49593pt too high) has occurred while \output is active [684] Underfull \hbox (badness 1173) in paragraph at lines 3844--3848 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [685] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3919--3919 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3948--3951 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699]) (./grDevices-pkg.tex [700] Chapter 4. [701] [702] [703] [704] [705] [706] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [707] Overfull \hbox (6.78088pt too wide) in paragraph at lines 470--470 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [708] [709] [710] [711] [712] [713] [714] [715] [716] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [717] Underfull \hbox (badness 1325) in paragraph at lines 1131--1137 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [718] Underfull \hbox (badness 10000) in paragraph at lines 1172--1174 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [719] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1224--1224 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [720] Underfull \hbox (badness 1173) in paragraph at lines 1266--1269 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [721] [722] [723] Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1526--1529 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [724] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [725] [726] [727] Underfull \hbox (badness 1565) in paragraph at lines 1754--1759 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1754--1759 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [728] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1837--1837 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [729] Underfull \hbox (badness 1184) in paragraph at lines 1878--1888 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1878--1888 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [731] [732] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [733] [734] Underfull \hbox (badness 2326) in paragraph at lines 2254--2264 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2254--2264 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2254--2264 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2254--2264 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [735] [736] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2357--2357 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [737] [738] [739] [740] [741] [742] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [743] [744] [745] [746] [747] [748] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3138--3138 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3139--3139 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3170--3172 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [749] Underfull \hbox (badness 10000) in paragraph at lines 3230--3235 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [750] [751] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3382--3382 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [752] [753] Underfull \hbox (badness 3525) in paragraph at lines 3489--3492 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 1968) in paragraph at lines 3503--3505 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [754] [755] [756] [757] Underfull \hbox (badness 5939) in paragraph at lines 3797--3802 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [758] [759] [760] [761] [762] [763] Underfull \hbox (badness 7576) in paragraph at lines 4170--4177 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4170--4177 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [764] [765] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4287--4287 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] Underfull \hbox (badness 1502) in paragraph at lines 4334--4339 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [766] [767] Underfull \hbox (badness 4765) in paragraph at lines 4493--4495 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if [768] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4507--4507 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 5077) in paragraph at lines 4547--4553 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [769] Underfull \hbox (badness 1342) in paragraph at lines 4563--4565 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [770] Underfull \hbox (badness 1874) in paragraph at lines 4640--4648 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [771] Underfull \hbox (badness 1755) in paragraph at lines 4707--4709 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [772] [773] Underfull \hbox (badness 7344) in paragraph at lines 4878--4880 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4889--4893 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [774] [775] Underfull \hbox (badness 1552) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5012--5014 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5044--5050 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [776] Underfull \hbox (badness 10000) in paragraph at lines 5070--5077 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [777] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5171--5171 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [778] [779] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5283--5283 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5289--5293 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [780] Underfull \hbox (badness 10000) in paragraph at lines 5369--5371 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [781] Underfull \hbox (badness 1072) in paragraph at lines 5405--5411 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [782] [783] [784] [785] [786] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5728--5728 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5741--5744 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 1189) in paragraph at lines 6138--6140 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 6236--6238 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6275--6282 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 6275--6282 \T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s ys-tems which have the Wine [795] Underfull \hbox (badness 3088) in paragraph at lines 6359--6363 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [796] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6404--6404 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] Underfull \hbox (badness 10000) in paragraph at lines 6436--6439 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [797] [798] Underfull \hbox (badness 5637) in paragraph at lines 6527--6533 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6560--6563 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [799] [800] [801] Underfull \hbox (badness 6157) in paragraph at lines 6717--6720 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6728--6730 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [802] [803] [804]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [805] [806] [807] [808] Underfull \hbox (badness 1412) in paragraph at lines 286--291 []\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [809] [810] [811] Underfull \hbox (badness 2726) in paragraph at lines 465--471 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [812] [813] [814] Underfull \hbox (badness 10000) in paragraph at lines 655--659 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 655--659 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if Underfull \hbox (badness 2735) in paragraph at lines 683--690 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [815] Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [816] [817] Underfull \hbox (badness 1062) in paragraph at lines 849--852 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [818] [819] [820] [821] [822] [823] [824] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1283--1283 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [825] Underfull \hbox (badness 1024) in paragraph at lines 1328--1336 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1356--1362 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1356--1362 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1362--1364 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1384--1388 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [826] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1432--1432 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1433--1433 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1440--1440 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [827] [828] [829] [830] [831] Underfull \hbox (badness 10000) in paragraph at lines 1740--1746 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [832] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1786--1786 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [833] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1869--1869 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [834] [835] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1998--1998 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2003--2003 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [836] [837] [838] [839] [840] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [841] [842] [843] [844] [845] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2617--2617 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [846] [847] Underfull \hbox (badness 5878) in paragraph at lines 2778--2782 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2803--2806 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [848] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2831--2831 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2835--2835 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [849] Underfull \hbox (badness 10000) in paragraph at lines 2887--2890 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [850] [851] [852] [853] Underfull \hbox (badness 1755) in paragraph at lines 3148--3152 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [854] Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [855] [856] [857] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3406--3406 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3425--3425 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3429--3429 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [858] [859] [860] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3606--3606 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3607--3607 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3644--3644 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [861] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3696--3696 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Underfull \vbox (badness 10000) has occurred while \output is active [862] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3716--3716 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3779--3783 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for [863] [864] [865] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [866] [867] Underfull \hbox (badness 3930) in paragraph at lines 4094--4096 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [868] [869] [870] [871] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [872] Underfull \hbox (badness 1286) in paragraph at lines 4402--4405 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4500--4500 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor)[] [874] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4504--4504 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [875] Underfull \hbox (badness 1264) in paragraph at lines 4622--4635 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [876] [877] Underfull \hbox (badness 7925) in paragraph at lines 4759--4765 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. [878] [879] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [880 ] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 [881 ] [882] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [883] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5197--5197 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5198--5198 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [884] [885] Underfull \hbox (badness 3954) in paragraph at lines 5299--5302 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5355--5359 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [886] [887] [888] [889] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5563--5563 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5564--5564 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5615--5619 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., Underfull \hbox (badness 1024) in paragraph at lines 5615--5619 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [890] [891] [892] [893] [894] [895] [896] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6048--6048 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [897] [898] [899] [900] [901] [902] Underfull \hbox (badness 10000) in paragraph at lines 6475--6477 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [903] [904] Underfull \hbox (badness 1028) in paragraph at lines 6569--6571 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [905 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6706--6706 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [906] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6737--6737 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] Underfull \hbox (badness 10000) in paragraph at lines 6859--6861 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6886--6886 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6892--6892 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [909] Underfull \hbox (badness 2600) in paragraph at lines 6952--6954 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [910] [911] [912] Underfull \hbox (badness 1881) in paragraph at lines 7141--7146 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7184--7184 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [914] [915] [916] [917] [918] [919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7571--7571 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7575--7575 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [920] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7587--7587 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [921] [922] [923] [924] [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7930--7930 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [926] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7937--7937 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [927] [928] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8108--8108 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8109--8109 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [929] [930] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8213--8213 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8224--8229 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [931] [932] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8328--8328 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8343--8343 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [933] [934] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [935] [936] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8647--8647 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [937] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8709--8715 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [938]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [939] Underfull \hbox (badness 1205) in paragraph at lines 8822--8824 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [940] [941] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8941--8941 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [942]) (./grid-pkg.tex Chapter 6. [943] [944] [945] [946] [947] [948] Underfull \hbox (badness 10000) in paragraph at lines 383--389 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 383--389 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1023--1023 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [959] Underfull \hbox (badness 1430) in paragraph at lines 1072--1077 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [960] [961] [962] Underfull \hbox (badness 3219) in paragraph at lines 1286--1289 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [963] [964] [965] [966] [967] [968] [969] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1673--1673 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [970] [971] [972] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1888--1888 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [973] Underfull \hbox (badness 2961) in paragraph at lines 1924--1929 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [974] Underfull \hbox (badness 1430) in paragraph at lines 1983--1988 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2012--2015 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [975] [976] [977] Underfull \hbox (badness 2894) in paragraph at lines 2219--2226 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [978] [979] [980] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2375--2375 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2387--2392 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [981] [982] [983] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2580--2580 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2612--2612 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [984] [985] [986] [987] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2852--2852 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [988] [989] [990] [991] [992] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3162--3162 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [993] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3258--3258 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [994] Underfull \hbox (badness 2799) in paragraph at lines 3292--3298 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [995] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3384--3384 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [996] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3391--3391 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [997] [998] [999] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3600--3600 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 1430) in paragraph at lines 4157--4162 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1009] [1010] [1011] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1012] Underfull \hbox (badness 1430) in paragraph at lines 4386--4391 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1013] [1014] [1015] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] Underfull \hbox (badness 10000) in paragraph at lines 5174--5176 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] Underfull \hbox (badness 3449) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1036] [1037] [1038] [1039] [1040] Underfull \hbox (badness 1867) in paragraph at lines 6172--6174 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 6209--6215 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1041] [1042] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1043] [1044] [1045] [1046] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6545--6545 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1047]) (./methods-pkg.tex [1048] Chapter 7. [1049] [1050] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1051] [1052] [1053] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1054] [1055] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1056] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1057] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1058] [1059] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1795--1795 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1797--1797 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1073] [1074] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1075] [1076] [1077] Underfull \hbox (badness 1132) in paragraph at lines 2215--2220 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1078] [1079] Underfull \hbox (badness 10000) in paragraph at lines 2329--2333 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2361--2361 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1080] [1081] [1082] Underfull \hbox (badness 3792) in paragraph at lines 2575--2578 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2606--2610 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1083] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2662--2662 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1084] [1085] [1086] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2881--2881 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1087] [1088] [1089] [1090] [1091] [1092] [1093] Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3404--3409 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1094] [1095] Underfull \hbox (badness 10000) in paragraph at lines 3532--3536 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1096] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3645--3654 [] [1097] [1098] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3765--3766 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 Underfull \hbox (badness 10000) in paragraph at lines 3812--3813 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1099] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3831--3832 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") Overfull \hbox (120.78088pt too wide) in paragraph at lines 3849--3850 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3911--3915 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 4138--4140 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1103] [1104] Underfull \hbox (badness 1629) in paragraph at lines 4250--4259 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4311--4311 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4312--4312 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4369--4369 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1107] [1108] Underfull \hbox (badness 1033) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1109] Underfull \hbox (badness 2126) in paragraph at lines 4577--4585 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1110] [1111] [1112] Underfull \hbox (badness 10000) in paragraph at lines 4814--4823 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1113] [1114] [1115] [1116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5198--5198 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1117] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5226--5226 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5240--5240 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1118] [1119] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1120] Underfull \hbox (badness 10000) in paragraph at lines 5466--5468 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1121] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1122] [1123] [1124] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1125] Underfull \hbox (badness 10000) in paragraph at lines 5760--5764 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5760--5764 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1126] Underfull \hbox (badness 10000) in paragraph at lines 5851--5855 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5851--5855 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1127] [1128] [1129] [1130] Underfull \hbox (badness 10000) in paragraph at lines 6213--6229 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1131] [1132] Underfull \hbox (badness 1248) in paragraph at lines 6346--6350 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6346--6350 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1133] Underfull \hbox (badness 4647) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1134] Underfull \hbox (badness 1072) in paragraph at lines 6578--6585 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1135] Underfull \hbox (badness 2875) in paragraph at lines 6650--6659 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6650--6659 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1136] Underfull \vbox (badness 10000) has occurred while \output is active [1137] [1138] [1139]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1140] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7012--7012 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7068--7075 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1141] [1142] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7203--7203 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1143]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1144] Underfull \hbox (badness 6708) in paragraph at lines 7312--7324 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7312--7324 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7312--7324 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1145] [1146] Underfull \hbox (badness 1694) in paragraph at lines 7475--7477 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7499--7502 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1147] [1148] Underfull \hbox (badness 10000) in paragraph at lines 7666--7673 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7666--7673 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] Underfull \hbox (badness 1052) in paragraph at lines 8492--8499 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1160] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8625--8625 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1161] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8700--8700 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1162] [1163] [1164] [1165] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1166] [1167] [1168] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9170--9170 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1169] [1170] Underfull \vbox (badness 2277) has occurred while \output is active [1171] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9432--9432 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1172] [1173] [1174] [1175] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9740--9740 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1176] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9850--9850 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1177] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9861--9861 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] Underfull \hbox (badness 10000) in paragraph at lines 10559--10561 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10567--10571 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1187] [1188] [1189] [1190]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1191] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1192] [1193] Underfull \hbox (badness 1024) in paragraph at lines 196--199 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1194] Underfull \hbox (badness 10000) in paragraph at lines 287--290 []\T1/ptm/m/n/10 Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.3.0 the de-fault wa s \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/10 ex-cept on Win-dows, but Underfull \hbox (badness 10000) in paragraph at lines 305--313 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1195] [1196] Underfull \hbox (badness 10000) in paragraph at lines 423--425 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1197] [1198] [1199] [1200] Underfull \hbox (badness 1917) in paragraph at lines 718--727 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 718--727 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1201] [1202] Underfull \hbox (badness 10000) in paragraph at lines 855--858 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1203] [1204] [1205] Underfull \hbox (badness 5388) in paragraph at lines 1048--1053 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from [1206] Underfull \hbox (badness 10000) in paragraph at lines 1072--1080 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1109--1109 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1207] [1208] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1225--1225 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1268--1271 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1209] Underfull \hbox (badness 3375) in paragraph at lines 1314--1316 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1210] [1211]) (./splines-pkg.tex [1212] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1213] [1214] [1215] [1216] [1217] [1218] [1219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1220] [1221] [1222] [1223] Overfull \hbox (25.98041pt too wide) in paragraph at lines 699--699 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1224] [1225] [1226]) (./stats-pkg.tex Chapter 10. [1227] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1228] [1229] [1230] [1231] [1232] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1233] [1234] [1235] [1236] [1237] [1238] [1239] Underfull \hbox (badness 1024) in paragraph at lines 848--850 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] Underfull \hbox (badness 10000) in paragraph at lines 1392--1394 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1248] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] Underfull \hbox (badness 10000) in paragraph at lines 2081--2086 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2081--2086 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2081--2086 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2087--2093 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2087--2093 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1258] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1259] [1260] [1261] [1262] Underfull \hbox (badness 1221) in paragraph at lines 2433--2438 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2433--2438 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1263] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1264] [1265] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2645--2645 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1266] [1267] [1268] [1269] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2885--2885 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1270] [1271] [1272] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3093--3095 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1273] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3140--3140 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3141--3141 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1274] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1275] [1276] [1277] [1278] [1279] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3531--3531 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1280] [1281] [1282] [1283] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3801--3801 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1284] [1285] [1286] [1287] [1288] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4086--4086 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4087--4087 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1289] [1290] [1291] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4322--4322 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1292] [1293] [1294] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4490--4490 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1295] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1296] [1297] [1298] [1299] [1300] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4942--4942 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4944--4944 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1301] [1302] Underfull \hbox (badness 7397) in paragraph at lines 5031--5035 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5031--5035 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1303] [1304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5165--5165 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5183--5183 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5210--5212 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by Underfull \hbox (badness 10000) in paragraph at lines 5215--5217 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1305] [1306] [1307] Underfull \hbox (badness 1436) in paragraph at lines 5393--5398 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5393--5398 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5393--5398 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1308] [1309] [1310] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5588--5588 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1311] Underfull \hbox (badness 1168) in paragraph at lines 5660--5665 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1312] [1313] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5754--5754 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1314] [1315] [1316] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5939--5939 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1317] [1318] Underfull \hbox (badness 10000) in paragraph at lines 6102--6107 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When [1319] [1320] [1321] Underfull \hbox (badness 5954) in paragraph at lines 6298--6300 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1322] Underfull \hbox (badness 2503) in paragraph at lines 6380--6383 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6384--6386 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6387--6392 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1323] Underfull \hbox (badness 7238) in paragraph at lines 6423--6426 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1324] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6458--6458 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6473--6473 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6488--6488 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1325] [1326] [1327] [1328] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6730--6730 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1329] [1330] Underfull \vbox (badness 10000) has occurred while \output is active [1331] [1332] [1333] [1334] Underfull \hbox (badness 10000) in paragraph at lines 7128--7132 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1335] Underfull \hbox (badness 6493) in paragraph at lines 7225--7228 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1336] [1337] Underfull \hbox (badness 10000) in paragraph at lines 7362--7365 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 10000) in paragraph at lines 7772--7777 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1344] [1345] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7910--7912 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1346] [1347] [1348] Underfull \hbox (badness 1210) in paragraph at lines 8127--8129 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1349] [1350] [1351] [1352] [1353] [1354] [1355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571 [] \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino mial()$mu_eta[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8593--8593 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8596--8596 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1356] [1357] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8734--8734 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1358] Underfull \hbox (badness 1859) in paragraph at lines 8773--8778 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1359] [1360] [1361] [1362] [1363] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9141--9141 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate S", "VeryS")))[] [1364] [1365] [1366] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2443) in paragraph at lines 9761--9767 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1373] [1374] [1375] Underfull \hbox (badness 3758) in paragraph at lines 9974--9977 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1376] [1377] [1378] [1379] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1380] Underfull \hbox (badness 4132) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1381] Underfull \hbox (badness 10000) in paragraph at lines 10377--10380 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1382] [1383] [1384] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1385] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1386] Underfull \hbox (badness 10000) in paragraph at lines 10700--10706 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10738--10743 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1387] [1388] Underfull \hbox (badness 2635) in paragraph at lines 10871--10874 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1389] [1390] [1391] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11073--11082 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1392] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11155--11155 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1393] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11188--11188 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11201--11205 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1394] [1395] [1396] Underfull \hbox (badness 7379) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1397] [1398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1399] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11587--11587 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11599--11599 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1400] Underfull \hbox (badness 1062) in paragraph at lines 11648--11653 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11665--11667 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1401] [1402] Underfull \hbox (badness 3623) in paragraph at lines 11816--11818 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1403] [1404] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11912--11912 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1405] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12005--12005 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1406] Underfull \hbox (badness 10000) in paragraph at lines 12053--12056 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1407] [1408] [1409] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1410] [1411] Underfull \hbox (badness 2753) in paragraph at lines 12345--12347 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1412] [1413] Underfull \hbox (badness 1292) in paragraph at lines 12470--12474 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1414] Underfull \hbox (badness 10000) in paragraph at lines 12583--12585 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12589--12593 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] Underfull \hbox (badness 4518) in paragraph at lines 13284--13289 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1426] [1427] [1428] Underfull \hbox (badness 10000) in paragraph at lines 13478--13482 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1429] [1430] Underfull \hbox (badness 6995) in paragraph at lines 13663--13665 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1431] [1432] [1433] Underfull \hbox (badness 1163) in paragraph at lines 13811--13819 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1434] Underfull \hbox (badness 4518) in paragraph at lines 13931--13936 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1435] [1436] Underfull \hbox (badness 10000) in paragraph at lines 14069--14073 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14069--14073 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1437] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14117--14117 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14118--14118 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1438] Underfull \hbox (badness 10000) in paragraph at lines 14173--14176 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14173--14176 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1439] [1440] [1441] [1442] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14459--14459 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14460--14460 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1443] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14510--14512 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14553--14553 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1444] [1445] [1446] [1447] [1448] [1449] [1450] Underfull \hbox (badness 2726) in paragraph at lines 14956--14959 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15671--15671 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1462] [1463] Underfull \hbox (badness 1014) in paragraph at lines 15809--15814 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1464] Underfull \hbox (badness 1648) in paragraph at lines 15869--15871 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 15883--15892 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 15883--15892 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1465] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15951--15951 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16504--16504 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1475] [1476] [1477] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16732--16732 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2772) in paragraph at lines 17167--17170 []\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate s. When Underfull \hbox (badness 10000) in paragraph at lines 17167--17170 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr /m/n/10 start \T1/ptm/m/n/10 is tried (if [1485] [1486] Underfull \hbox (badness 2359) in paragraph at lines 17287--17289 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1487] Underfull \vbox (badness 10000) has occurred while \output is active [1488] Underfull \vbox (badness 10000) has occurred while \output is active [1489] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17459--17459 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1490] Underfull \hbox (badness 10000) in paragraph at lines 17539--17543 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1491] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17619--17619 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1492] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17666--17666 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17713--17713 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Underfull \hbox (badness 1248) in paragraph at lines 18203--18206 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1127) in paragraph at lines 18216--18220 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1501] Underfull \hbox (badness 1478) in paragraph at lines 18224--18228 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and Underfull \hbox (badness 2042) in paragraph at lines 18277--18279 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1502] [1503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18373--18373 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1504] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18415--18415 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18448--18448 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18451--18451 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1505] Underfull \hbox (badness 2564) in paragraph at lines 18486--18497 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18486--18497 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1506] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18549--18549 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1507] [1508] [1509] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18764--18764 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1510] Underfull \hbox (badness 1337) in paragraph at lines 18840--18843 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1511] [1512] [1513] [1514] [1515] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19156--19156 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1516] [1517] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19244--19244 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19247--19247 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1518] Underfull \hbox (badness 3049) in paragraph at lines 19326--19330 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1519] [1520] [1521] [1522] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19569--19569 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19576--19578 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19579--19582 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1523] Underfull \hbox (badness 1107) in paragraph at lines 19637--19639 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1524] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19692--19692 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1525] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19699--19699 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] Underfull \hbox (badness 10000) in paragraph at lines 19749--19752 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 19749--19752 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1526] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19793--19793 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1527] [1528] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19918--19918 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1529] Underfull \hbox (badness 10000) in paragraph at lines 19981--19983 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1530] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20029--20029 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) Underfull \hbox (badness 10000) in paragraph at lines 20084--20086 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1531] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20121--20121 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] Overfull \hbox (25.98041pt too wide) in paragraph at lines 20951--20951 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1545] Underfull \hbox (badness 6859) in paragraph at lines 21018--21025 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21029--21035 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Overfull \hbox (78.78088pt too wide) in paragraph at lines 22044--22044 [] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) %in % c("Pr(", "p-v"),[] [1562] [1563] [1564] [1565] [1566] Underfull \hbox (badness 1337) in paragraph at lines 22367--22373 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Overfull \hbox (133.98029pt too wide) in paragraph at lines 22912--22912 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1575] [1576] [1577] Underfull \hbox (badness 1028) in paragraph at lines 23052--23055 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1578] Underfull \hbox (badness 10000) in paragraph at lines 23162--23165 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23162--23165 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1579] Underfull \hbox (badness 10000) in paragraph at lines 23217--23219 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1580] Underfull \hbox (badness 10000) in paragraph at lines 23279--23281 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1581] [1582] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23381--23381 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1583] [1584] [1585] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23601--23601 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1586] [1587] Underfull \hbox (badness 10000) in paragraph at lines 23747--23750 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1588] Underfull \hbox (badness 2134) in paragraph at lines 23798--23802 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 23811--23811 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1589] [1590] [1591] [1592] [1593] [1594] [1595] Underfull \hbox (badness 2591) in paragraph at lines 24268--24274 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][ ][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/ ptm/m/n/10 mod-els (with ex-am- [1596] [1597] [1598] Underfull \hbox (badness 1867) in paragraph at lines 24465--24467 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1599] Underfull \hbox (badness 10000) in paragraph at lines 24478--24482 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24478--24482 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Overfull \hbox (20.58041pt too wide) in paragraph at lines 24514--24514 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1600] [1601] [1602] Underfull \hbox (badness 2495) in paragraph at lines 24704--24713 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1603] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24786--24786 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 24793--24795 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1604] [1605] Overfull \hbox (25.98041pt too wide) in paragraph at lines 24880--24880 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 24905--24905 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 24908--24908 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1606] Underfull \hbox (badness 10000) in paragraph at lines 24950--24955 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 24950--24955 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1607] Underfull \hbox (badness 2980) in paragraph at lines 25095--25097 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1608] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25131--25131 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] [1609] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25180--25180 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Underfull \vbox (badness 10000) has occurred while \output is active [1610] [1611] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25303--25303 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1612] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25370--25370 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1613] [1614] [1615] [1616] [1617] [1618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 25746--25746 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 25799--25802 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1619] [1620] Overfull \hbox (31.3804pt too wide) in paragraph at lines 25925--25925 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 25926--25926 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1621] Underfull \hbox (badness 2922) in paragraph at lines 25992--25997 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1622] Underfull \hbox (badness 2922) in paragraph at lines 26054--26059 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 3240) in paragraph at lines 26066--26070 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff [1623] Underfull \hbox (badness 2922) in paragraph at lines 26111--26116 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1624] Underfull \hbox (badness 2922) in paragraph at lines 26172--26178 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1625] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26194--26194 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26210--26210 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1626] [1627] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26324--26324 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) Overfull \hbox (4.38043pt too wide) in paragraph at lines 26347--26347 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response and gradient[] [1628] Underfull \hbox (badness 2922) in paragraph at lines 26385--26390 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1629] Underfull \hbox (badness 2922) in paragraph at lines 26441--26446 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 2922) in paragraph at lines 26499--26504 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1630] Underfull \hbox (badness 2922) in paragraph at lines 26554--26559 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26575--26575 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Underfull \hbox (badness 6493) in paragraph at lines 26623--26628 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1632] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26649--26649 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26651--26651 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1633] [1634] [1635] [1636] [1637] [1638] [1639] Underfull \hbox (badness 10000) in paragraph at lines 27147--27150 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27147--27150 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1640] [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 3396) in paragraph at lines 27576--27578 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1647] [1648] [1649] Underfull \hbox (badness 2237) in paragraph at lines 27753--27755 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1650] [1651] Underfull \hbox (badness 2591) in paragraph at lines 27917--27919 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1652] Underfull \hbox (badness 2237) in paragraph at lines 27963--27966 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1653] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28036--28036 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1654] [1655] Underfull \hbox (badness 3407) in paragraph at lines 28144--28148 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1656] [1657] Underfull \hbox (badness 1337) in paragraph at lines 28277--28281 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1658] [1659] Underfull \hbox (badness 10000) in paragraph at lines 28394--28397 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1660] [1661] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28523--28523 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28551--28551 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1662] Underfull \hbox (badness 1616) in paragraph at lines 28577--28580 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1663] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28656--28656 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1664] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28733--28733 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1665] Underfull \hbox (badness 5050) in paragraph at lines 28769--28774 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1666] Underfull \hbox (badness 2205) in paragraph at lines 28822--28827 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29417--29417 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1675] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29418--29418 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1676] [1677] [1678] [1679] Underfull \hbox (badness 10000) in paragraph at lines 29703--29707 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 29703--29707 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 29714--29714 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29715--29715 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1680] [1681] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29841--29841 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29850--29850 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] [1682] [1683] [1684] [1685] Underfull \hbox (badness 1337) in paragraph at lines 30067--30071 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] Underfull \hbox (badness 1337) in paragraph at lines 30551--30555 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1694] Underfull \hbox (badness 1946) in paragraph at lines 30628--30633 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 30650--30652 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1695] [1696] [1697] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30975--30975 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1700] Underfull \hbox (badness 6775) in paragraph at lines 31032--31037 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1701] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31095--31095 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31110--31110 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s parse = TRUE))[] [1702]) (./stats4-pkg.tex Chapter 11. [1703] [1704] [1705] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1706] [1707] [1708]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1709] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1710] [1711]) (./tcltk-pkg.tex [1712] Chapter 12. [1713] [1714] [1715] [1716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1717] [1718] [1719] Underfull \vbox (badness 10000) has occurred while \output is active [1720] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1732]) (./tools-pkg.tex Chapter 13. [1733] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1734] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1735] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1736] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1737] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1738] [1739] [1740] Underfull \hbox (badness 10000) in paragraph at lines 543--544 [][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer / en / opentype / [1741] [1742] [1743] [1744] [1745] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 905--905 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1747] Overfull \hbox (31.3804pt too wide) in paragraph at lines 953--953 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1748] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1749] [1750] Underfull \hbox (badness 5431) in paragraph at lines 1128--1131 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1751] Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1204--1207 []\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he r-it-ing from class [1752] [1753] Underfull \hbox (badness 10000) in paragraph at lines 1344--1347 []\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1754] [1755] [1756] [1757] [1758] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1667--1667 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1670--1670 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1677--1682 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1759] [1760] [1761]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1762] [1763] [1764] [1765] Underfull \hbox (badness 2644) in paragraph at lines 2149--2155 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgMacros \T1/ptm/m/n/10 func-tion firs t looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-age Overfull \hbox (101.58032pt too wide) in paragraph at lines 2183--2183 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1766] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2184--2184 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2211--2218 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2211--2218 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2211--2218 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1767] Underfull \hbox (badness 1342) in paragraph at lines 2263--2269 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1768] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2339--2339 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2352--2358 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1769] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2385--2385 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2394--2394 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2411--2411 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1770] [1771] [1772] [1773] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2676--2676 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1774] Underfull \hbox (badness 2486) in paragraph at lines 2721--2729 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1775] [1776] [1777] [1778] [1779] Underfull \hbox (badness 1072) in paragraph at lines 3099--3101 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1780] [1781] [1782] [1783] [1784] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3435--3435 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1785] [1786] [1787] [1788] Underfull \hbox (badness 4108) in paragraph at lines 3679--3686 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1789] [1790] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3779--3779 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3782--3782 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3816--3822 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1791] [1792] Underfull \hbox (badness 7832) in paragraph at lines 3938--3941 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1793] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4013--4013 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1794] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1795] [1796] [1797] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4210--4210 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4221--4224 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4237--4242 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4245--4251 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4245--4251 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1798] Underfull \hbox (badness 3758) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList \T1/ptm/m/n/10 ob- Underfull \hbox (badness 2865) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie d (for in-stance if there was [1799] [1800] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4457--4457 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4458--4458 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4470--4473 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', [1801] Underfull \hbox (badness 1742) in paragraph at lines 4474--4484 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4509--4515 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4509--4515 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 4537--4541 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1802] [1803] [1804]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1805] [1806] [1807] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1808] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1809] [1810] Underfull \hbox (badness 1946) in paragraph at lines 453--457 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1811] Overfull \hbox (0.78088pt too wide) in paragraph at lines 503--503 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 510--510 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 512--512 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] [1812] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 546--552 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1813] Underfull \hbox (badness 4505) in paragraph at lines 660--666 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1814] [1815] Underfull \hbox (badness 1603) in paragraph at lines 777--783 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 777--783 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1816] Overfull \hbox (6.78088pt too wide) in paragraph at lines 834--834 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1817] Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1818] Underfull \hbox (badness 10000) in paragraph at lines 1004--1007 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1819] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1087--1087 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1820] [1821] [1822] [1823] [1824] [1825] Underfull \hbox (badness 1859) in paragraph at lines 1458--1467 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1826] [1827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1559--1559 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1594--1594 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1828] [1829] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1740--1740 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1760--1760 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1830] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1816--1816 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1831] Underfull \hbox (badness 2213) in paragraph at lines 1857--1860 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1832] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via [1833] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1992--1992 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2015--2015 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1834] [1835] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2135--2135 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1836] Underfull \hbox (badness 1082) in paragraph at lines 2209--2213 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; Underfull \hbox (badness 10000) in paragraph at lines 2246--2248 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1837] Underfull \hbox (badness 1057) in paragraph at lines 2278--2285 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1838] [1839] [1840] Underfull \hbox (badness 10000) in paragraph at lines 2467--2469 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1841] [1842] [1843] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2703--2707 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1844] Underfull \hbox (badness 10000) in paragraph at lines 2757--2760 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set [1845] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2829--2829 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1846] Underfull \hbox (badness 2452) in paragraph at lines 2905--2908 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1847] [1848] [1849] [1850] [1851] [1852] [1853] Underfull \hbox (badness 1072) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1854] Underfull \hbox (badness 10000) in paragraph at lines 3441--3446 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3441--3446 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3441--3446 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1855] Underfull \hbox (badness 4660) in paragraph at lines 3563--3566 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to [1856] [1857] [1858] Underfull \hbox (badness 1565) in paragraph at lines 3772--3776 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of Underfull \hbox (badness 10000) in paragraph at lines 3793--3799 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1859] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3855--3855 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1860] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3883--3890 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1861] [1862] [1863] [1864] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4203--4203 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1865] [1866]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4274 ...mat Unordered and Ordered Lists}{format} [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1881] Underfull \hbox (badness 10000) in paragraph at lines 5311--5313 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1882] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1883] [1884] [1885] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1886] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 5612--5615 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1887] [1888] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1889] Underfull \hbox (badness 5091) in paragraph at lines 5870--5872 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL [1890] Overfull \hbox (44.55087pt too wide) in paragraph at lines 5886--5891 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 5899--5906 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1891] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., Underfull \hbox (badness 10000) in paragraph at lines 6016--6020 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , [1892] Underfull \hbox (badness 2376) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1314) in paragraph at lines 6089--6096 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1893] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6133--6133 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 6169--6173 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 6181--6184 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [1894] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6227--6227 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1895] [1896] Underfull \hbox (badness 4132) in paragraph at lines 6346--6348 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1897] [1898] [1899] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6504--6504 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1900] [1901] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6647--6647 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1902] Underfull \hbox (badness 10000) in paragraph at lines 6687--6689 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1903] [1904] Underfull \hbox (badness 10000) in paragraph at lines 6828--6830 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 6833--6835 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1905] [1906] [1907] Underfull \hbox (badness 1859) in paragraph at lines 7056--7059 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1908] Underfull \hbox (badness 1655) in paragraph at lines 7138--7141 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 7149--7149 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] [1909] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7153--7153 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 7161--7161 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1910] Underfull \hbox (badness 10000) in paragraph at lines 7246--7250 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1911] [1912] [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1915] [1916] [1917] Underfull \hbox (badness 10000) in paragraph at lines 7683--7688 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7683--7688 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 10000) in paragraph at lines 7690--7693 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7690--7693 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1918] [1919] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7806--7806 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7807--7807 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1920] [1921] [1922] [1923] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1924] Underfull \hbox (badness 10000) in paragraph at lines 8145--8149 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8145--8149 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1925] Underfull \hbox (badness 10000) in paragraph at lines 8258--8262 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8258--8262 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1926] [1927] Underfull \hbox (badness 10000) in paragraph at lines 8321--8325 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8321--8325 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1928] [1929] [1930] [1931] Underfull \hbox (badness 5203) in paragraph at lines 8652--8655 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1932] [1933] [1934] Underfull \hbox (badness 1776) in paragraph at lines 8878--8885 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set Overfull \hbox (30.78088pt too wide) in paragraph at lines 8902--8902 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1935] [1936] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9063--9063 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1937] [1938] [1939] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9244--9244 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [1940] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9330--9330 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] [1941] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9333--9333 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9338--9338 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1942] Underfull \hbox (badness 1077) in paragraph at lines 9410--9413 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [1943] [1944] [1945] [1946] [1947] [1948] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9850--9850 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1949] Underfull \hbox (badness 10000) in paragraph at lines 9937--9939 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1950] [1951] Underfull \hbox (badness 2181) in paragraph at lines 10060--10064 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10072--10076 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1952] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10090--10090 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10094--10094 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1953] [1954] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10226--10226 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1955] [1956] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10366--10366 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [1957] Underfull \hbox (badness 8075) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via Underfull \hbox (badness 6725) in paragraph at lines 10479--10488 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10479--10488 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10479--10488 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10479--10488 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1958] [1959] Underfull \hbox (badness 3646) in paragraph at lines 10605--10607 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [1960] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10643--10643 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1961] [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 10824--10828 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10855--10861 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1964] Underfull \hbox (badness 2012) in paragraph at lines 10950--10956 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use Underfull \hbox (badness 2096) in paragraph at lines 10963--10965 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 10966--10968 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10973--10976 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 10977--10980 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if [1965] Overfull \hbox (6.78088pt too wide) in paragraph at lines 11031--11031 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 11049--11060 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1966] [1967] Underfull \hbox (badness 2846) in paragraph at lines 11136--11146 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1968] [1969] Underfull \hbox (badness 10000) in paragraph at lines 11275--11278 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un- Underfull \hbox (badness 10000) in paragraph at lines 11275--11278 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11292--11295 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1970] [1971] Underfull \hbox (badness 2158) in paragraph at lines 11374--11377 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [1972] [1973] Underfull \hbox (badness 3333) in paragraph at lines 11557--11559 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [1974] [1975] [1976] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11722--11722 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 5970) in paragraph at lines 11755--11758 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11755--11758 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11766--11775 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1977] Overfull \hbox (36.7804pt too wide) in paragraph at lines 11810--11810 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [1978] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11841--11841 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 11848--11848 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11850--11850 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 12018--12020 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [1981] [1982] [1983] Underfull \hbox (badness 4492) in paragraph at lines 12175--12182 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12175--12182 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12175--12182 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [1984] [1985] Underfull \hbox (badness 2020) in paragraph at lines 12335--12351 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12335--12351 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [1986] Underfull \hbox (badness 5022) in paragraph at lines 12434--12438 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12441--12444 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 12441--12444 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] Underfull \hbox (badness 4467) in paragraph at lines 12950--12952 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 12963--12967 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to [1995] Overfull \hbox (36.87935pt too wide) in paragraph at lines 12977--12981 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 3557) in paragraph at lines 12983--12985 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12986--12988 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13037--13042 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with [1996] Underfull \hbox (badness 10000) in paragraph at lines 13045--13048 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13099--13099 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [1997] [1998] [1999] Underfull \hbox (badness 10000) in paragraph at lines 13287--13290 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; [2000] Overfull \hbox (42.18039pt too wide) in paragraph at lines 13303--13303 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13337--13337 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2001] Underfull \hbox (badness 1454) in paragraph at lines 13364--13368 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13389--13392 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and [2002] Underfull \hbox (badness 10000) in paragraph at lines 13434--13436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion Underfull \hbox (badness 3271) in paragraph at lines 13446--13450 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2003] [2004] [2005]) [2006] [2007] [2008] (./KernSmooth-pkg.tex Chapter 15. [2009] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2010] [2011] [2012] [2013] [2014] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2015] [2016] [2017] [2018]) (./MASS-pkg.tex Chapter 16. [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 7256) in paragraph at lines 1603--1605 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2415--2415 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2053] [2054] [2055] [2056] Underfull \hbox (badness 6559) in paragraph at lines 2693--2696 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2057] [2058] [2059] Underfull \hbox (badness 7362) in paragraph at lines 2863--2868 \T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 , Underfull \hbox (badness 3557) in paragraph at lines 2899--2907 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2899--2907 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2060] [2061] Underfull \hbox (badness 4686) in paragraph at lines 3031--3033 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 3045--3049 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2062] [2063] [2064] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3226--3226 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3233--3235 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2065] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1845) in paragraph at lines 4162--4164 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2078] [2079] [2080] [2081] [2082] [2083] [2084] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2085] [2086] Underfull \hbox (badness 10000) in paragraph at lines 4810--4813 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2087] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4888--4891 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2088] [2089] [2090] [2091] [2092] Underfull \hbox (badness 5681) in paragraph at lines 5288--5290 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5292--5295 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2093] Underfull \hbox (badness 1975) in paragraph at lines 5341--5343 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5927--5927 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2102] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5988--5988 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2103] [2104]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} [2105] Underfull \hbox (badness 1783) in paragraph at lines 6248--6252 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2106] [2107] [2108] [2109] Underfull \vbox (badness 10000) has occurred while \output is active [2110] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6546--6546 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2111] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2112] [2113] [2114] [2115] [2116] [2117] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7073--7073 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7090--7090 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7097--7104 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2118] Underfull \hbox (badness 10000) in paragraph at lines 7113--7115 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7168--7174 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2119] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7238--7238 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2120] [2121] Underfull \hbox (badness 5091) in paragraph at lines 7347--7350 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2122] [2123] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7477--7477 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2124] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7542--7542 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2125] [2126] [2127] [2128] [2129] [2130] Underfull \hbox (badness 4686) in paragraph at lines 7980--7982 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 7996--8000 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2131] [2132] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8099--8099 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8123--8127 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n /10 NA\T1/ptm/m/n/10 s are found. The [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9502--9502 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2153] Underfull \hbox (badness 1158) in paragraph at lines 9629--9632 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly), [2154] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9711--9711 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9713--9713 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9716--9716 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167]) (./Matrix-pkg.tex [2168] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2169] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2170] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2171] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2172] [2173] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2174] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2175] [2176] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2177] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2178] [2179] [2180] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2181] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2182]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2183pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] [2184] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2185] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2186] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2187] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2188] Underfull \hbox (badness 6445) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3861) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and [2189]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2190] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2191] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2192] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2193] [2194] [2195] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2196] [2197] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2198] Underfull \hbox (badness 4713) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2199] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2200] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2201] Underfull \hbox (badness 2707) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2202] Overfull \hbox (120.78088pt too wide) in paragraph at lines 2663--2663 []\T1/pcr/m/n/10 .symDiagonal(n, x = rep.int(1,n), uplo = "U", kind = if(is. logical(x)) "l" else "d")[] Overfull \hbox (120.78088pt too wide) in paragraph at lines 2664--2664 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind = if(is. logical(x)) "l" else "d")[] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2203] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2204] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 3803) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a [2205] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2206] [2207] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2208] Underfull \hbox (badness 1168) in paragraph at lines 3358--3361 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2209] [2210] Underfull \hbox (badness 4967) in paragraph at lines 3523--3527 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix", ...) \T1/ptm/m/n/10 or Overfull \hbox (2.39853pt too wide) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . [2211] Underfull \hbox (badness 6364) in paragraph at lines 3570--3573 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2212] [2213] Underfull \hbox (badness 10000) in paragraph at lines 3720--3725 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3720--3725 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 10000) in paragraph at lines 3730--3732 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3732--3735 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2214] Underfull \hbox (badness 10000) in paragraph at lines 3840--3843 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3840--3843 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the Underfull \hbox (badness 10000) in paragraph at lines 3843--3846 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3843--3846 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion [2215] Underfull \hbox (badness 6364) in paragraph at lines 3847--3850 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2216] Underfull \hbox (badness 4060) in paragraph at lines 3967--3970 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2217] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4007--4007 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4075--4079 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class [2218] Underfull \hbox (badness 10000) in paragraph at lines 4084--4087 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 4084--4087 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4089--4093 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2219] [2220] [2221] [2222] Underfull \hbox (badness 10000) in paragraph at lines 4377--4382 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2223] [2224] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4511--4511 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4514--4514 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4528--4528 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2225] [2226] Underfull \hbox (badness 10000) in paragraph at lines 4683--4685 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2227] [2228] Underfull \hbox (badness 10000) in paragraph at lines 4830--4835 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2229] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4911--4911 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4913--4913 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4917--4917 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4924--4924 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2230] [2231] Underfull \hbox (badness 4120) in paragraph at lines 5063--5066 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2232] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5100--5100 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5105--5105 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5112--5112 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5115--5115 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2233] Underfull \hbox (badness 1817) in paragraph at lines 5204--5213 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 5637) in paragraph at lines 5246--5248 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2234] Underfull \hbox (badness 3138) in paragraph at lines 5272--5274 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2235] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5339--5339 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] Underfull \hbox (badness 1603) in paragraph at lines 5360--5362 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2236] [2237] [2238] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5597--5597 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2239] Underfull \hbox (badness 10000) in paragraph at lines 5678--5681 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5689--5689 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2240] Underfull \hbox (badness 1622) in paragraph at lines 5726--5731 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5726--5731 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2241] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5787--5787 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5788--5788 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5795--5795 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2242] [2243] Underfull \hbox (badness 1062) in paragraph at lines 5924--5927 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 2809) in paragraph at lines 5953--5956 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2244] Underfull \hbox (badness 2635) in paragraph at lines 6065--6070 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6065--6070 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class [2245] Underfull \hbox (badness 10000) in paragraph at lines 6073--6076 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6183--6193 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6183--6193 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2246] Underfull \hbox (badness 1184) in paragraph at lines 6265--6268 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2247] Underfull \hbox (badness 10000) in paragraph at lines 6363--6366 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2248] Underfull \hbox (badness 10000) in paragraph at lines 6438--6441 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2249] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6454--6454 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Underfull \hbox (badness 2443) in paragraph at lines 6493--6499 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6493--6499 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6514--6517 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2250] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6584--6584 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2251] [2252] Underfull \hbox (badness 6268) in paragraph at lines 6720--6723 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2253] Underfull \hbox (badness 5036) in paragraph at lines 6744--6748 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6744--6748 \T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e mpty'' [][]sparse-Ma-trix[][][], as does [2254]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6837 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6917--6920 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6922--6925 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6922--6925 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6940--6943 Underfull \hbox (badness 7326) in paragraph at lines 6950--6952 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re -lies on a cor-rect [2255]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7013 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7121 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7221 ...tcrossprod}{matrix-products}{tcrossprod} [2256] Underfull \hbox (badness 1881) in paragraph at lines 7319--7325 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2257pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7381 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7381 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7392--7395 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 7392--7395 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7395--7400 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7404--7406 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7406--7408 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7410--7411 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2258] [2259] Underfull \hbox (badness 1062) in paragraph at lines 7591--7594 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2260] Underfull \hbox (badness 2809) in paragraph at lines 7625--7628 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2261] Underfull \hbox (badness 10000) in paragraph at lines 7677--7679 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter [2262] Underfull \hbox (badness 1406) in paragraph at lines 7717--7721 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7717--7721 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2263] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7815--7815 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2264] Underfull \hbox (badness 2635) in paragraph at lines 7880--7885 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7880--7885 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7888--7891 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2265] [2266] Underfull \hbox (badness 10000) in paragraph at lines 8082--8084 []\T1/ptm/m/n/10 fast [2267]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8122 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8122 \HeaderA{norm}{Matrix Norms}{norm} [2268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8209--8209 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8210--8210 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8211--8211 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8324--8334 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2269] Underfull \hbox (badness 1184) in paragraph at lines 8395--8398 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2270] Underfull \hbox (badness 10000) in paragraph at lines 8485--8488 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2271] Underfull \hbox (badness 10000) in paragraph at lines 8561--8564 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2272] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8577--8577 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2273] Underfull \hbox (badness 10000) in paragraph at lines 8687--8689 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8703--8705 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8709--8713 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2274] [2275] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8788--8788 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8793--8793 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8798--8798 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8821--8831 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8821--8831 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2276] [2277]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8922 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8968--8971 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 8995--8995 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] [2278] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9006--9006 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9024--9024 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9032--9032 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=1e-15))## just = X, incl. co rrect colnames[] [2279] Underfull \hbox (badness 10000) in paragraph at lines 9085--9091 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9102--9105 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2280] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9174--9174 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9195--9195 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9196--9196 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2281]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco nd}) has been already used, duplicate ignored \relax l.9215 ... the Reciprocal Condition Number}{rcond} [2282] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9328--9328 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2283] [2284] [2285] Underfull \hbox (badness 10000) in paragraph at lines 9511--9513 []\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably Underfull \hbox (badness 1325) in paragraph at lines 9517--9525 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2286] [2287] Underfull \hbox (badness 1558) in paragraph at lines 9662--9665 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2288] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9724--9724 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9728--9728 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2289]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9790 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9887--9887 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9892--9892 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2290] Underfull \hbox (badness 6047) in paragraph at lines 9927--9939 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9944--9947 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9949--9950 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9953--9960 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9953--9960 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 9966--9976 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 9966--9976 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2291] Underfull \hbox (badness 1194) in paragraph at lines 10000--10002 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10014--10017 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10023--10024 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10029--10031 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10033--10034 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10041--10044 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10059--10059 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10063--10063 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2292] Underfull \hbox (badness 10000) in paragraph at lines 10084--10087 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10112--10114 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10120--10123 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the [2293] Underfull \hbox (badness 10000) in paragraph at lines 10131--10135 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10131--10135 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10142--10144 []\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in -di-cat-ing if the re-sult must be a [2294] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10219--10219 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10220--10220 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10221--10221 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2295] [2296] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10405--10405 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10406--10406 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2297] Underfull \hbox (badness 4621) in paragraph at lines 10446--10450 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2298] Underfull \hbox (badness 10000) in paragraph at lines 10522--10525 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10534--10534 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10538--10538 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10539--10539 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10544--10544 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10547--10547 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2299] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10570--10570 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10571--10571 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10597--10597 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10599--10599 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10601--10601 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2300] Underfull \hbox (badness 10000) in paragraph at lines 10694--10702 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10715--10719 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2301] Underfull \hbox (badness 10000) in paragraph at lines 10745--10749 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10785 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2302] [2303] Underfull \hbox (badness 1430) in paragraph at lines 10915--10917 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10943--10943 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 10971--10973 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2304] Underfull \hbox (badness 2970) in paragraph at lines 11104--11110 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11104--11110 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2305] Underfull \hbox (badness 10000) in paragraph at lines 11155--11158 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11177--11180 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2306] Underfull \hbox (badness 10000) in paragraph at lines 11195--11200 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11210--11212 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2307] [2308] Underfull \hbox (badness 3525) in paragraph at lines 11328--11332 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11335--11341 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2309] Underfull \hbox (badness 10000) in paragraph at lines 11430--11434 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11430--11434 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11446--11451 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 1259) in paragraph at lines 11446--11451 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11454--11459 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2310] Underfull \hbox (badness 2057) in paragraph at lines 11526--11528 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2311] [2312] Underfull \hbox (badness 6641) in paragraph at lines 11612--11615 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11652--11656 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11652--11656 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2313] Underfull \hbox (badness 7649) in paragraph at lines 11759--11761 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2314] [2315] [2316] Underfull \hbox (badness 7362) in paragraph at lines 11960--11962 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2317] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11998--11998 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11999--11999 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2318] [2319] Underfull \hbox (badness 6910) in paragraph at lines 12249--12251 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2320] [2321] [2322]) (./boot-pkg.tex Chapter 18. [2323] [2324] [2325] [2326] [2327] [2328] [2329] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2330] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2331] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2332] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2333] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2334] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2335] [2336] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues [2337] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2338] [2339] [2340] [2341] [2342] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2343] [2344] [2345] [2346] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2347] [2348] [2349] [2350] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] Underfull \vbox (badness 10000) has occurred while \output is active [2351] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2352] [2353] [2354] [2355] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. [2356] Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2357] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2358] [2359] [2360] [2361] [2362] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2363] [2364] [2365] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2366] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2367] [2368] [2369] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2370] [2371] [2372] [2373] [2374] [2375] [2376] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2377] [2378] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2379] [2380] [2381] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2383] [2384] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2385] [2386] [2387] [2388] [2389] [2390] [2391] [2392] [2393] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2394] [2395] [2396] [2397] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2399] [2400] [2401] [2402] [2403] [2404] [2405] [2406] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2407] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2408] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2409] [2410] [2411] [2412] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2413] [2414] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2415] [2416] [2417] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2418] [2419] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427]) (./class-pkg.tex [2428] Chapter 19. [2429] [2430] [2431] [2432] [2433] [2434] [2435] [2436] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2437] [2438] [2439] [2440] [2441] [2442] [2443] [2444]) (./cluster-pkg.tex Chapter 20. [2445] Underfull \hbox (badness 3098) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2446] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2447] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2448] [2449] Underfull \vbox (badness 10000) has occurred while \output is active [2450] [2451] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2452] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2453] Overfull \hbox (66.78088pt too wide) in paragraph at lines 636--636 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2454] Underfull \hbox (badness 3078) in paragraph at lines 682--685 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2455] Underfull \hbox (badness 2941) in paragraph at lines 771--774 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2456] Overfull \hbox (9.78043pt too wide) in paragraph at lines 809--809 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2457] Underfull \hbox (badness 10000) in paragraph at lines 857--859 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2458] Overfull \hbox (24.78088pt too wide) in paragraph at lines 922--922 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2459] Underfull \hbox (badness 4872) in paragraph at lines 968--970 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 982--986 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2460] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1089--1089 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2461] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1144--1144 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2462] Underfull \hbox (badness 4144) in paragraph at lines 1176--1180 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2463] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1252--1252 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1258--1258 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2464] [2465] Underfull \hbox (badness 10000) in paragraph at lines 1397--1402 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*, cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1445--1448 Underfull \hbox (badness 10000) in paragraph at lines 1462--1466 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , [2466] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1486--1486 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1496--1496 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2467] Underfull \hbox (badness 5741) in paragraph at lines 1536--1539 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1602--1602 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2469] Underfull \hbox (badness 5008) in paragraph at lines 1719--1727 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where [2470] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1810--1810 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] [2471] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1829--1829 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2472] [2473] [2474] [2475] Underfull \hbox (badness 10000) in paragraph at lines 2137--2139 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2148--2151 Underfull \hbox (badness 3179) in paragraph at lines 2162--2168 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2476] [2477] [2478] Underfull \hbox (badness 10000) in paragraph at lines 2320--2323 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2479] Underfull \hbox (badness 1292) in paragraph at lines 2388--2391 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2397--2399 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2420--2423 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2480] [2481] [2482] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2634--2634 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2483] [2484] [2485] Underfull \hbox (badness 1067) in paragraph at lines 2820--2825 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2486] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2487] [2488] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2982--2982 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2489] [2490] [2491] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3178--3178 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2492] Underfull \hbox (badness 10000) in paragraph at lines 3246--3249 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2493] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3296--3296 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3297--3297 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2494] [2495] [2496] Underfull \hbox (badness 10000) in paragraph at lines 3482--3485 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for Underfull \hbox (badness 3471) in paragraph at lines 3482--3485 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2497] Underfull \hbox (badness 10000) in paragraph at lines 3545--3550 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2498] Underfull \hbox (badness 4621) in paragraph at lines 3607--3612 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3607--3612 \T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1 /ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider Underfull \hbox (badness 6268) in paragraph at lines 3619--3622 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2499] [2500] [2501] Underfull \hbox (badness 10000) in paragraph at lines 3804--3807 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3835--3838 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2502] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3888--3888 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3899--3901 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2503] [2504] [2505] [2506] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4092--4092 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4094--4094 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4123--4128 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2507] Underfull \hbox (badness 10000) in paragraph at lines 4190--4198 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2508] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4232--4232 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4241--4241 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4243--4243 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4246--4246 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4248--4248 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4262--4262 [] \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t olerance = 0))[] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2517] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2518] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2519] [2520] [2521]) (./foreign-pkg.tex [2522] Chapter 22. [2523] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2524] [2525] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2526] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2527] [2528] [2529] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2530] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli cated_"\T1/ptm/m/n/10 ) if [2531] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2532] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2534] [2535] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2536] [2537] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2538] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2539] [2540] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2541] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2542] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2543] Underfull \hbox (badness 6725) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by [2544]) (./lattice-pkg.tex Chapter 23. [2545] [2546] [2547] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2548] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2549] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2550] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2551] [2552] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2553] [2554] [2555] [2556] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2557] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2558] [2559] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2560] [2561] [2562] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2563] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2564] Underfull \vbox (badness 10000) has occurred while \output is active [2565] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2566] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2567] Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2568] [2569] [2570] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2571] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2572] [2573] [2574] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2575] [2576] [2577] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2578] [2579] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2580] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2581] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast er[][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2883--2885 []\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T 1/ptm/m/n/10 when [2582] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2583] [2584] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2585] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2586] [2587] [2588] [2589]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2590] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2591] [2592] [2593] [2594] [2595] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2596] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2597] [2598] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4105--4109 \T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se t-tings (ob-tained by [2599] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2600] [2601] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl ot.polygon \T1/ptm/m/n/10 and [2602] [2603] [2604] [2605] [2606] [2607] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2608] [2609] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2610] [2611] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2612] [2613] [2614] [2615] [2616] [2617] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2618] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef t of pan-els us-ing Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2619] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh ich is to draw a strip ap-pro-pri-ate for [2620] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2621] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2622] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2623] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are used (in com-bi-na-tion with [2624] [2625] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2626] [2627] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2628] [2629] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2630] [2631] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2632] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2633] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2634] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2635] [2636] [2637] [2638] [2639] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2640] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2641] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu nc-tion is passed [2642] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2643] [2644] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2645] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2646] [2647] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2648] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2649] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2650] [2651] [2652] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2653] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2662] [2663] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2664] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2665] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2666] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2667] [2668] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2669] [2670] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2671] Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left, right, left.name, right.name, condition Overfull \hbox (104.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name , right.x.name, right.y.name, condition [2672] [2673] [2674] [2675] [2676] [2677] [2678] Underfull \hbox (badness 4205) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2679] [2680] [2681]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2682] [2683] [2684] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes \T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2685] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2686]) (./mgcv-pkg.tex Chapter 24. [2687] [2688] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2689] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2690] [2691] [2692] Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2693] [2694] [2695] [2696] Underfull \hbox (badness 2922) in paragraph at lines 595--596 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2697] [2698] Underfull \hbox (badness 1158) in paragraph at lines 666--668 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2699] Underfull \hbox (badness 1259) in paragraph at lines 729--730 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2700] Underfull \vbox (badness 10000) has occurred while \output is active [2701] [2702] [2703] [2704] [2705] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1078--1078 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1084--1084 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] [2706] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1091--1091 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1093--1093 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",ylim=c(0,1),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2707] [2708] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1231--1231 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2709] [2710] [2711] [2712] [2713] [2714] [2715] [2716] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1686--1686 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2717] [2718] Underfull \vbox (badness 4913) has occurred while \output is active [2719] [2720] [2721] [2722] Underfull \hbox (badness 1052) in paragraph at lines 2061--2069 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2078--2078 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2090--2093 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also [2723] Underfull \hbox (badness 1142) in paragraph at lines 2103--2107 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2129--2134 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2724] [2725] [2726] Underfull \hbox (badness 1043) in paragraph at lines 2294--2300 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2727] [2728] Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2729] Underfull \vbox (badness 10000) has occurred while \output is active [2730] Underfull \vbox (badness 10000) has occurred while \output is active [2731] [2732] [2733] [2734] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2748--2748 [] \T1/pcr/m/n/10 keepData=FALSE,scale.est="fletcher",edge.correct= FALSE)[] [2735] [2736] [2737] [2738] [2739] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3075--3075 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3078--3078 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2740] [2741] [2742] [2743] [2744] [2745] Underfull \hbox (badness 5189) in paragraph at lines 3439--3443 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2746] Underfull \vbox (badness 10000) has occurred while \output is active [2747] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3556--3556 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2748] [2749] Underfull \hbox (badness 1184) in paragraph at lines 3725--3729 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4171--4171 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2758] [2759] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4321--4321 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2760] [2761] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4415--4415 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] Underfull \hbox (badness 1142) in paragraph at lines 4446--4450 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2762] Underfull \hbox (badness 10000) in paragraph at lines 4515--4524 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2763] [2764] Underfull \hbox (badness 5970) in paragraph at lines 4632--4638 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4632--4638 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2765] Underfull \vbox (badness 10000) has occurred while \output is active [2766] [2767] [2768] Underfull \hbox (badness 1577) in paragraph at lines 4912--4915 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 4919--4920 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2769] [2770] [2771] [2772] [2773] [2774] [2775] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5314--5314 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2776] [2777] [2778] [2779] [2780] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5638--5638 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2781] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5640--5640 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5661--5665 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2782] [2783] [2784] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5797--5797 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in i,n.chains=1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5828--5828 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in i,n.chains=1)[] Underfull \vbox (badness 10000) has occurred while \output is active [2785] [2786] Overfull \hbox (72.78088pt too wide) in paragraph at lines 5902--5902 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2787] [2788] [2789] Underfull \vbox (badness 10000) has occurred while \output is active [2790] [2791] [2792] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6281--6281 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [2793] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6308--6308 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2794] [2795] [2796] [2797] [2798] [2799] Underfull \vbox (badness 4366) has occurred while \output is active [2800] [2801] Underfull \hbox (badness 1242) in paragraph at lines 6851--6852 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2802] [2803] [2804] [2805] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7001--7001 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7020--7020 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2806] [2807] [2808] [2809] [2810] [2811] [2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] Underfull \vbox (badness 10000) has occurred while \output is active [2824] [2825] Underfull \hbox (badness 10000) in paragraph at lines 8240--8243 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8240--8243 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8240--8243 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2826] Underfull \hbox (badness 10000) in paragraph at lines 8296--8299 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8296--8299 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2827] [2828] [2829] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8516--8516 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8517--8517 [] \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla b=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8520--8520 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2830] [2831] [2832] Underfull \hbox (badness 1629) in paragraph at lines 8675--8680 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2833] [2834] [2835] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8876--8876 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2836] [2837] [2838] [2839] [2840] [2841] Underfull \vbox (badness 10000) has occurred while \output is active [2842] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9304--9304 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2843] Underfull \hbox (badness 1205) in paragraph at lines 9342--9344 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9342--9344 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9348--9353 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2844] Underfull \hbox (badness 1205) in paragraph at lines 9432--9434 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9432--9434 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2845] Underfull \hbox (badness 10000) in paragraph at lines 9501--9504 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9501--9504 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2846] [2847] [2848] Underfull \hbox (badness 1253) in paragraph at lines 9631--9633 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2849] [2850] Underfull \vbox (badness 10000) has occurred while \output is active [2851] Underfull \hbox (badness 1946) in paragraph at lines 9809--9816 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 9809--9816 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 9809--9816 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 9817--9820 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 9817--9820 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2852] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9883--9883 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] [2853] Underfull \hbox (badness 10000) in paragraph at lines 9912--9915 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2854] [2855] [2856] [2857] [2858] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10199--10199 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2859] [2860] [2861] [2862] [2863] Underfull \vbox (badness 10000) has occurred while \output is active [2864] Underfull \hbox (badness 3861) in paragraph at lines 10540--10543 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10547--10547 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10560--10564 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2865] Underfull \hbox (badness 10000) in paragraph at lines 10600--10604 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2866] [2867] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10741--10741 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 10752--10757 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2868] [2869] Underfull \hbox (badness 1803) in paragraph at lines 10829--10833 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 10841--10853 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 10858--10862 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 10858--10862 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2870] [2871] [2872] Underfull \hbox (badness 6876) in paragraph at lines 11053--11059 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like [2873] Underfull \hbox (badness 10000) in paragraph at lines 11094--11095 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2874] [2875] Underfull \hbox (badness 10000) in paragraph at lines 11212--11213 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2876] [2877] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11277--11277 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11288--11288 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11289--11289 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11294--11294 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11300--11300 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11301--11301 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] Underfull \vbox (badness 10000) has occurred while \output is active [2878] Underfull \hbox (badness 10000) in paragraph at lines 11370--11372 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11370--11372 \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs", ...) \T1/ptm/m/n/10 or [2879] [2880] Underfull \hbox (badness 10000) in paragraph at lines 11498--11499 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2881] [2882] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11579--11579 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11580--11580 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2883] Underfull \hbox (badness 7613) in paragraph at lines 11618--11621 \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p tm/m/n/10 pro-duced by the [2884] [2885] Underfull \hbox (badness 10000) in paragraph at lines 11727--11728 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2886] [2887] [2888] [2889] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11964--11964 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] Underfull \hbox (badness 10000) in paragraph at lines 12009--12011 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2890] [2891] Underfull \vbox (badness 10000) has occurred while \output is active [2892] Underfull \hbox (badness 10000) in paragraph at lines 12168--12171 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12168--12171 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12168--12171 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2893] [2894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12250--12250 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12295--12301 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12295--12301 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2895] [2896] [2897] Underfull \vbox (badness 10000) has occurred while \output is active [2898] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12509--12509 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2899] [2900] Underfull \hbox (badness 10000) in paragraph at lines 12612--12620 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 12638--12639 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2901] [2902] [2903] [2904] Underfull \hbox (badness 3396) in paragraph at lines 12899--12902 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2905] Underfull \hbox (badness 10000) in paragraph at lines 12944--12946 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2906] [2907] [2908] [2909] Underfull \hbox (badness 10000) in paragraph at lines 13168--13171 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13168--13171 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [2910] Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [2911] [2912] [2913] [2914] Underfull \hbox (badness 2158) in paragraph at lines 13442--13442 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2915] Overfull \hbox (48.78088pt too wide) in paragraph at lines 13517--13517 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2916] [2917] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13651--13651 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2918] [2919] Underfull \hbox (badness 4846) in paragraph at lines 13779--13782 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [2920] [2921] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] [2931] [2932] [2933] Underfull \hbox (badness 10000) in paragraph at lines 14604--14612 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 14604--14612 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2934] [2935] [2936] [2937] Overfull \hbox (24.78088pt too wide) in paragraph at lines 14876--14876 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2938] [2939] [2940] [2941] [2942] [2943] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15170--15170 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15171--15171 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15183--15183 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2944] [2945] [2946]) (./nlme-pkg.tex Chapter 25. [2947] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2948] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2949] [2950] [2951] [2952] [2953] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2954] [2955] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [2964] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [2965] [2966] [2967] [2968] [2969] [2970] [2971] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [2972] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [2973] [2974] [2975] [2976] [2977] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [2978] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [2979] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [2980] [2981] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [2982] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001] [3002] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3003] [3004] [3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3027] [3028] [3029] [3030] [3031] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3032] [3033] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041] [3042] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3043] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3044] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3045] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3046] [3047] [3048] [3049] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3050] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , [3051] Underfull \hbox (badness 10000) in paragraph at lines 6717--6719 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3052] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6747--6747 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3053] [3054] [3055] Underfull \hbox (badness 10000) in paragraph at lines 6990--6997 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3056] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7007--7007 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7015--7015 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7037--7039 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3057] [3058] [3059] Underfull \hbox (badness 10000) in paragraph at lines 7252--7257 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3060] [3061] [3062] Underfull \hbox (badness 10000) in paragraph at lines 7404--7412 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7404--7412 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 1817) in paragraph at lines 7404--7412 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7427--7430 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3063] [3064] [3065] Underfull \hbox (badness 3354) in paragraph at lines 7642--7644 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3066] [3067] [3068] [3069] [3070] [3071] Underfull \hbox (badness 1642) in paragraph at lines 8034--8056 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3072] [3073] Underfull \hbox (badness 10000) in paragraph at lines 8154--8171 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8154--8171 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8197--8197 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8206--8228 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3074] [3075] [3076] [3077] [3078] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8471--8471 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8516--8518 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3079] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8554--8554 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8561 \aliasA{sigma}{lmeObject}{sigma} [3080] [3081] [3082] Underfull \hbox (badness 10000) in paragraph at lines 8722--8734 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] Underfull \hbox (badness 10000) in paragraph at lines 9313--9320 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9324--9324 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3092] Underfull \hbox (badness 6300) in paragraph at lines 9406--9409 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3093] [3094] [3095] [3096]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3097] Underfull \hbox (badness 10000) in paragraph at lines 9695--9698 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9739--9742 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9739--9742 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3098] [3099] [3100] Underfull \hbox (badness 2435) in paragraph at lines 9913--9918 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3101] [3102] [3103] [3104] [3105] Underfull \hbox (badness 7291) in paragraph at lines 10203--10205 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3106] [3107] [3108] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10419--10419 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3109] Underfull \hbox (badness 1596) in paragraph at lines 10448--10474 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3110] [3111] [3112] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10624--10624 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3113] [3114] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10775--10775 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] [3115] Underfull \hbox (badness 10000) in paragraph at lines 10821--10823 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Underfull \hbox (badness 1092) in paragraph at lines 10833--10836 []\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr /m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used Overfull \hbox (9.78043pt too wide) in paragraph at lines 10856--10856 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3116] [3117] [3118] [3119] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11112--11112 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] Underfull \hbox (badness 6268) in paragraph at lines 11891--11901 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3132] [3133] [3134] [3135] Underfull \hbox (badness 10000) in paragraph at lines 12152--12158 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3136] [3137] [3138] [3139] [3140] Underfull \hbox (badness 6876) in paragraph at lines 12474--12476 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3141] [3142] Underfull \hbox (badness 2452) in paragraph at lines 12630--12637 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3143] Underfull \hbox (badness 10000) in paragraph at lines 12695--12701 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13647--13647 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3158] Underfull \hbox (badness 10000) in paragraph at lines 13674--13677 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 6016) in paragraph at lines 13702--13705 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13702--13705 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13709--13712 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13717--13724 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13717--13724 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner [3159] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13774--13774 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13781--13784 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13781--13784 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle [3160] Underfull \hbox (badness 4582) in paragraph at lines 13809--13812 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13809--13812 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13813--13816 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3161] Underfull \hbox (badness 10000) in paragraph at lines 13889--13892 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 1472) in paragraph at lines 13914--13921 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3162] Underfull \hbox (badness 10000) in paragraph at lines 13983--13985 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3163] [3164] [3165] [3166] Underfull \hbox (badness 1540) in paragraph at lines 14198--14203 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14245--14247 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3167] [3168] [3169] [3170] [3171] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14489--14489 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15142 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15142 ...Extract Random Effects}{random.effects} [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] Underfull \hbox (badness 1009) in paragraph at lines 15799--15808 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3191] [3192] [3193] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15946--15946 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3194] [3195] [3196] [3197] Underfull \hbox (badness 10000) in paragraph at lines 16224--16242 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16224--16242 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3198] Underfull \hbox (badness 10000) in paragraph at lines 16281--16287 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3199] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16312--16312 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3200] [3201] [3202] [3203] [3204] [3205] [3206] Underfull \hbox (badness 1728) in paragraph at lines 16801--16804 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3207] [3208] [3209] [3210] [3211] Underfull \hbox (badness 1867) in paragraph at lines 17136--17145 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3212] Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , [3213] [3214] [3215] [3216] Underfull \hbox (badness 10000) in paragraph at lines 17447--17454 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 10000) in paragraph at lines 17977--17987 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17977--17987 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18015--18020 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3225] Underfull \hbox (badness 3579) in paragraph at lines 18079--18084 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3226] Underfull \hbox (badness 3579) in paragraph at lines 18142--18147 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3227] Underfull \hbox (badness 1577) in paragraph at lines 18203--18205 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18205--18210 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3228] Underfull \hbox (badness 3579) in paragraph at lines 18268--18273 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3229] Underfull \hbox (badness 10000) in paragraph at lines 18301--18310 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18301--18310 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18340--18345 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3230] [3231] [3232] Underfull \hbox (badness 1009) in paragraph at lines 18489--18498 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3233] [3234] Underfull \hbox (badness 1009) in paragraph at lines 18623--18632 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3243] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3244] [3245] [3246] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3247] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3248] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3249] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3250]) (./rpart-pkg.tex Chapter 27. [3251] [3252] [3253] [3254] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3255] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3256] [3257] [3258] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3259] [3260] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3261] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3262] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3263] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3264] [3265] [3266] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3267] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3268] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3269] [3270] [3271] [3272] [3273] [3274] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3275] [3276] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3277] [3278] [3279]) (./spatial-pkg.tex [3280] Chapter 28. [3281] [3282] [3283] [3284] [3285] [3286] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3287] [3288] [3289] [3290] [3291] [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299]) (./survival-pkg.tex [3300] Chapter 29. [3301] [3302] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3303] [3304] Overfull \hbox (42.78088pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho d, rownames) Overfull \hbox (42.78088pt too wide) in paragraph at lines 279--279 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho d, rownames)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.319 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.319 ... Myelogenous Leukemia survival data}{aml} [3305] [3306] Overfull \hbox (9.78043pt too wide) in paragraph at lines 416--416 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 418--418 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3307] Overfull \hbox (6.78088pt too wide) in paragraph at lines 455--455 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3308] [3309] Underfull \vbox (badness 10000) has occurred while \output is active [3310] Overfull \hbox (36.78088pt too wide) in paragraph at lines 654--654 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 655--655 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3311] [3312] Overfull \hbox (9.78043pt too wide) in paragraph at lines 798--798 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3313] [3314] [3315] Underfull \hbox (badness 1097) in paragraph at lines 968--970 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 988--988 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3316] [3317] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1103--1103 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3318]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1171 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3319] [3320] [3321] [3322] [3323] [3324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1623--1623 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3325] [3326] [3327] [3328] [3329] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1988--1988 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3330] [3331] [3332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2237--2237 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3333] [3334] [3335] [3336] [3337] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2554--2554 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Underfull \hbox (badness 1389) in paragraph at lines 2567--2569 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3338] Underfull \hbox (badness 1048) in paragraph at lines 2621--2623 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3339] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2698--2698 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] [3340] [3341] [3342] [3343] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2945--2945 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3344] [3345] [3346] [3347] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3211--3211 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3348] [3349] [3350] [3351] Underfull \vbox (badness 10000) has occurred while \output is active [3352] [3353] [3354] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3620--3620 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc ale=1,[] [3355] [3356] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3809--3809 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3357] [3358] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3925--3925 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3359] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4015--4015 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3360] [3361] [3362] Underfull \hbox (badness 1852) in paragraph at lines 4163--4165 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3363] [3364] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4297--4297 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4298--4298 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3365] [3366] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4462--4462 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3367] Underfull \hbox (badness 1540) in paragraph at lines 4517--4520 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4564--4564 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3368] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4585--4585 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3369] [3370] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4732--4732 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] [3371] Underfull \vbox (badness 10000) has occurred while \output is active [3372] [3373] [3374] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5017--5017 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response" \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 \T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n /10 . See the La-TeX doc-u-men-ta-tion [3375] [3376] [3377] [3378] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5302--5302 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5303--5303 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] [3379] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5358--5358 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3380] [3381] [3382] [3383] [3384] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5693--5693 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5694--5694 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3385] [3386] [3387] [3388] Overfull \hbox (54.78088pt too wide) in paragraph at lines 5995--5995 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3389] [3390] [3391] [3392] Underfull \hbox (badness 10000) in paragraph at lines 6255--6264 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3393] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6365--6365 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] [3394] Underfull \hbox (badness 1038) in paragraph at lines 6407--6413 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival Underfull \hbox (badness 3000) in paragraph at lines 6429--6431 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, [3395] Overfull \hbox (48.78088pt too wide) in paragraph at lines 6459--6459 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3396] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6545--6545 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3397] [3398] [3399] Underfull \hbox (badness 10000) in paragraph at lines 6770--6775 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , Overfull \hbox (18.78088pt too wide) in paragraph at lines 6791--6791 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T RUE, id,[] [3400] [3401] [3402] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7007--7007 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3403] Underfull \hbox (badness 6332) in paragraph at lines 7114--7119 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3404] [3405] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7294--7294 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3406] [3407] [3408] [3409] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3410] Underfull \hbox (badness 1354) in paragraph at lines 7622--7626 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3411] [3412] Underfull \hbox (badness 2035) in paragraph at lines 7798--7805 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 7798--7805 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 7798--7805 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3413] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7874--7874 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3414] [3415] [3416] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8032--8032 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3417] [3418] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8164--8164 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8167--8167 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3419] [3420] [3421] [3422] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8464--8464 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8465--8465 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8471--8471 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8473--8473 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3423] [3424] [3425] [3426] Underfull \vbox (badness 10000) has occurred while \output is active [3427] [3428]) (./fullrefman.ind [3429] [3430] [3431] [3432] [3433] [3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2186--2188 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2188--2190 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2190--2192 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in 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cbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 5902--5904 []\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 5904--5906 []\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method [3482] Overfull \hbox (10.01662pt too wide) in paragraph at lines 6072--6074 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Underfull \vbox (badness 1484) has occurred while \output is active Underfull \vbox (badness 1117) has occurred while \output is active [3483] [3484] [3485] Overfull \hbox (50.8567pt too wide) in paragraph at lines 6443--6445 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 6445--6447 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 6447--6449 []\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method Overfull \hbox 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coerce,dgeMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6541--6543 []\T1/pcr/m/n/10 coerce,dgeMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6543--6545 []\T1/pcr/m/n/10 coerce,dgeMatrix,dtrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6545--6547 []\T1/pcr/m/n/10 coerce,dgeMatrix,lgeMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 6549--6551 []\T1/pcr/m/n/10 coerce,dgeMatrix,triangularMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 6551--6553 []\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6553--6555 []\T1/pcr/m/n/10 coerce,dgTMatrix,dgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6555--6557 []\T1/pcr/m/n/10 coerce,dgTMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6557--6559 []\T1/pcr/m/n/10 coerce,dgTMatrix,dsTMatrix-method 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too wide) in paragraph at lines 7097--7099 []\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7101--7103 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7103--7105 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7105--7107 []\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7107--7109 []\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7109--7111 []\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7113--7115 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7115--7117 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7117--7119 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coerce,ngTMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7137--7139 []\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7143--7145 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7145--7147 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7147--7149 []\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7149--7151 []\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method [3493] Overfull \hbox (50.8567pt too wide) in paragraph at lines 7151--7153 []\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7165--7167 []\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7167--7169 []\T1/pcr/m/n/10 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coerce,nsparseVector,isparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7189--7191 []\T1/pcr/m/n/10 coerce,nsparseVector,lsparseVector-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (56.8567pt too wide) in paragraph at lines 7191--7193 []\T1/pcr/m/n/10 coerce,nsparseVector,zsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7193--7195 []\T1/pcr/m/n/10 coerce,nspMatrix,dspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7195--7197 []\T1/pcr/m/n/10 coerce,nspMatrix,lspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7197--7199 []\T1/pcr/m/n/10 coerce,nspMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7199--7201 []\T1/pcr/m/n/10 coerce,nspMatrix,nsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7201--7203 []\T1/pcr/m/n/10 coerce,nsTMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in 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coerce,ntCMatrix,dsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7225--7227 []\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7229--7231 []\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method [3494] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7231--7233 []\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7235--7237 []\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7237--7239 []\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7239--7241 []\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7241--7243 []\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7243--7245 []\T1/pcr/m/n/10 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lines 7389--7391 []\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7391--7393 []\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7393--7395 []\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7395--7397 []\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7397--7399 []\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7399--7401 []\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method [3496] Underfull \vbox (badness 1348) has occurred while \output is active Overfull \hbox (62.8567pt too wide) in paragraph at lines 7510--7512 []\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7516--7518 []\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 7528--7530 []\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7530--7532 []\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 7544--7546 []\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method [3497] [3498] [3499] Overfull \hbox (14.8567pt too wide) in paragraph at lines 7888--7890 []\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 7890--7892 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 7892--7894 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 7894--7896 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (32.8567pt too 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determinant,sparseMatrix,logical-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8396--8398 []\T1/pcr/m/n/10 determinant,sparseMatrix,missing-method [3504] [3505] Overfull \hbox (10.01662pt too wide) in paragraph at lines 8617--8619 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Underfull \vbox (badness 1226) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 8667--8669 []\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8669--8671 []\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method [3506] [3507] Overfull \hbox (46.01662pt too wide) in paragraph at lines 8874--8876 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3508] Overfull \hbox (8.8567pt too wide) in paragraph at lines 9082--9084 []\T1/pcr/m/n/10 expand,MatrixFactorization-method Overfull \hbox (10.01662pt too wide) in 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groupGenericFunctionWithTrace-class [3517] [3518] [3519] Underfull \vbox (badness 1484) has occurred while \output is active [3520] Overfull \hbox (8.8567pt too wide) in paragraph at lines 10761--10763 []\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 10763--10765 []\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 10771--10773 []\T1/pcr/m/n/10 is.infinite,nsparseVector-method Underfull \vbox (badness 1117) has occurred while \output is active [3521] Overfull \hbox (2.8567pt too wide) in paragraph at lines 10906--10908 []\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10912--10914 []\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 10914--10916 []\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method [3522] Overfull \hbox (8.8567pt too wide) in paragraph at lines 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[]\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method [3523] Overfull \hbox (20.8567pt too wide) in paragraph at lines 11089--11091 []\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11093--11095 []\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11095--11097 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11097--11099 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 11099--11101 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 11101--11103 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11103--11105 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11105--11107 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11107--11109 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11109--11111 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 11113--11115 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11115--11117 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11117--11119 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11119--11121 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11121--11123 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method Underfull \vbox (badness 1117) has occurred while \output is active [3524] [3525] [3526] Overfull \hbox (50.8567pt too wide) in paragraph at lines 11578--11580 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11584--11586 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11586--11588 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11588--11590 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11590--11592 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11592--11594 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11598--11600 []\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11608--11610 []\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11610--11612 []\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 11612--11614 []\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 11614--11616 []\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11616--11618 []\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method Underfull \vbox (badness 2903) has occurred while \output is active [3527] Overfull \hbox (2.8567pt too wide) in paragraph at lines 11624--11626 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11634--11636 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 11636--11638 []\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11644--11646 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11646--11648 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11648--11650 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 11650--11652 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11652--11654 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method Underfull \vbox (badness 3302) has occurred while \output is active [3528] [3529] [3530] [3531] Overfull \hbox (52.01662pt too wide) in paragraph at lines 12279--12281 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3532] [3533] [3534] Overfull \hbox (8.8567pt too wide) in paragraph at lines 12604--12606 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 12616--12618 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 12618--12620 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12624--12626 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 12642--12644 []\T1/pcr/m/n/10 norm,ldenseMatrix,character-method Underfull \vbox (badness 1824) has occurred while \output is active Overfull \hbox (14.8567pt too wide) in paragraph at lines 12648--12650 []\T1/pcr/m/n/10 norm,ndenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 12650--12652 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3535] Overfull \hbox (26.8567pt too wide) in paragraph at lines 12826--12828 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method [3536] Overfull \hbox (20.8567pt too wide) in paragraph at lines 12832--12834 []\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12844--12846 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 12846--12848 []\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 12848--12850 []\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12850--12852 []\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 12852--12854 []\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (38.8567pt too wide) in paragraph at lines 12872--12874 []\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12874--12876 []\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12890--12892 []\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12910--12912 []\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active [3537] Overfull \hbox (38.8567pt too wide) in paragraph at lines 12912--12914 []\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12932--12934 []\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12940--12942 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12944--12946 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12946--12948 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 12948--12950 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Underfull \vbox (badness 4328) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 12968--12970 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12970--12972 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12972--12974 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 12974--12976 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12978--12980 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12982--12984 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12986--12988 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3538] Overfull \hbox (46.01662pt too wide) in paragraph at lines 13092--13094 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 13112--13114 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3539] [3540] [3541] [3542] [3543] [3544] Overfull \hbox (46.01662pt too wide) in paragraph at lines 13936--13938 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13939--13941 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13941--13943 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13943--13945 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13945--13947 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13947--13949 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 13949--13951 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13951--13953 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13953--13955 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13955--13957 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 13959--13961 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13961--13963 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13963--13965 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13965--13967 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13967--13969 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13969--13971 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3545] Underfull \vbox (badness 3769) has occurred while \output is active [3546] Overfull \hbox (4.01662pt too wide) in paragraph at lines 14205--14207 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 14274--14276 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3547] [3548] [3549] Overfull \hbox (26.8567pt too wide) in paragraph at lines 14660--14662 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14669--14671 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14671--14673 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14673--14675 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14675--14677 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 14685--14687 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 14694--14696 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method [3550] Overfull \hbox (32.8567pt too wide) in paragraph at lines 14708--14710 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14714--14716 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3551] Overfull \hbox (26.8567pt too wide) in paragraph at lines 14956--14958 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14958--14960 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14960--14962 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14962--14964 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 14966--14968 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14968--14970 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14970--14972 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14972--14974 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 14974--14976 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14976--14978 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14978--14980 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14984--14986 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Underfull \vbox (badness 2564) has occurred while \output is active [3552] Overfull \hbox (2.8567pt too wide) in paragraph at lines 14988--14990 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14998--15000 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15002--15004 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15004--15006 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15006--15008 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 15008--15010 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15010--15012 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15012--15014 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 15014--15016 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15040--15042 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15042--15044 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15044--15046 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15046--15048 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15050--15052 []\T1/pcr/m/n/10 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rcond,sparseMatrix,character-method [3553] Underfull \vbox (badness 1484) has occurred while \output is active [3554] [3555] [3556] [3557] Overfull \hbox (20.8567pt too wide) in paragraph at lines 15738--15740 []\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15740--15742 []\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15744--15746 []\T1/pcr/m/n/10 Schur,generalMatrix,logical-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15746--15748 []\T1/pcr/m/n/10 Schur,generalMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15752--15754 []\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15754--15756 []\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 15756--15758 []\T1/pcr/m/n/10 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replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc} Output written on fullrefman.pdf (3634 pages, 9563808 bytes). Transcript written on fullrefman.log. This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./fullrefman.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded. 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Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m /n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 338--341 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] Underfull \hbox (badness 2359) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 533--539 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15] Overfull \hbox (0.78088pt too wide) in paragraph at lines 857--857 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20] [21] [22] [23] Underfull \hbox (badness 5862) in paragraph at lines 1378--1384 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1632--1632 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1648--1654 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1648--1654 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of [27] Underfull \hbox (badness 1303) in paragraph at lines 1658--1661 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 2865) in paragraph at lines 1760--1764 []\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/ m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then Underfull \hbox (badness 10000) in paragraph at lines 1764--1766 []\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1901--1901 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1936--1938 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1939--1941 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2193--2193 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [35] [36] Underfull \hbox (badness 1107) in paragraph at lines 2326--2328 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [37] [38] [39] [40] [41] Underfull \hbox (badness 5878) in paragraph at lines 2658--2663 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2658--2663 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [57] [58] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3848--3848 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [59] [60] [61] [62] Underfull \hbox (badness 4927) in paragraph at lines 4071--4075 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4071--4075 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [63] [64] Underfull \hbox (badness 4595) in paragraph at lines 4215--4218 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [65] [66] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Underfull \hbox (badness 1199) in paragraph at lines 4400--4406 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- [67] Underfull \hbox (badness 2573) in paragraph at lines 4411--4414 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [68] Underfull \hbox (badness 10000) in paragraph at lines 4491--4496 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4491--4496 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4491--4496 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [69] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4570--4570 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [70] [71] [72] [73] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [74] [75] [76] [77] [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 5212--5220 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [80] [81] [82] [83] [84] [85] [86] [87] Underfull \hbox (badness 1796) in paragraph at lines 5758--5766 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [88] [89] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5952--5952 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 5954--5954 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5955--5955 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [90] [91] Underfull \hbox (badness 1635) in paragraph at lines 6116--6119 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class [92] Underfull \hbox (badness 3009) in paragraph at lines 6120--6123 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing Underfull \hbox (badness 1102) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6151--6159 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [93] [94] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6299--6299 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [95] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6341--6343 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [96] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6483--6486 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [97] [98] [99] Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6666--6668 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 1067) in paragraph at lines 6708--6715 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [100] [101] Underfull \vbox (badness 10000) has occurred while \output is active [102] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6894--6894 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [103] [104] Underfull \hbox (badness 1231) in paragraph at lines 7019--7025 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [105] [106] [107] Underfull \hbox (badness 10000) in paragraph at lines 7230--7232 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [108] [109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7375--7375 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [110] Underfull \hbox (badness 4595) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [111] [112] [113] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [114] [115] Underfull \hbox (badness 8132) in paragraph at lines 7714--7718 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7714--7718 \T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , but this can be changed by set-ting Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1062) in paragraph at lines 7733--7743 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be Overfull \hbox (4.63962pt too wide) in paragraph at lines 7765--7769 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [116] Underfull \hbox (badness 7451) in paragraph at lines 7804--7814 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7804--7814 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [117] [118] [119] [120] [121] Underfull \hbox (badness 10000) in paragraph at lines 8211--8223 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8211--8223 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [122] [123] [124] Underfull \hbox (badness 5802) in paragraph at lines 8420--8424 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a [125] [126] [127] Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [128] [129] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8728--8728 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8730--8730 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [130] [131] Underfull \hbox (badness 4254) in paragraph at lines 8891--8895 []\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so urce \T1/ptm/m/n/10 at-tribute), use [132] Underfull \hbox (badness 1132) in paragraph at lines 8951--8958 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [133] Underfull \hbox (badness 1603) in paragraph at lines 9064--9067 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1917) in paragraph at lines 9664--9669 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [143] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9719--9719 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9720--9720 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [144] Underfull \hbox (badness 1168) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [145] [146] Underfull \hbox (badness 2828) in paragraph at lines 9960--9964 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 9960--9964 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ [147] [148] [149] [150] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10201--10201 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [151] Underfull \hbox (badness 1629) in paragraph at lines 10275--10279 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [152] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [153] Underfull \hbox (badness 3690) in paragraph at lines 10389--10397 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10398--10400 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than Underfull \hbox (badness 3735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [154] [155] [156] Underfull \hbox (badness 10000) in paragraph at lines 10624--10627 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [157] [158] [159] [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 5288) in paragraph at lines 11306--11308 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11316--11321 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [166] Underfull \hbox (badness 10000) in paragraph at lines 11376--11378 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [167] [168] Underfull \hbox (badness 4569) in paragraph at lines 11493--11497 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11493--11497 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [169] [170] Underfull \hbox (badness 10000) in paragraph at lines 11608--11610 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as Underfull \hbox (badness 2790) in paragraph at lines 11651--11653 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [171] [172] [173] Underfull \hbox (badness 4048) in paragraph at lines 11822--11832 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 11822--11832 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [174] [175] [176] Underfull \hbox (badness 5460) in paragraph at lines 12070--12079 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12070--12079 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [177] [178] [179] [180] [181] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12444--12444 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [182] [183] [184] [185] Underfull \hbox (badness 5119) in paragraph at lines 12729--12732 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [186] [187] Underfull \hbox (badness 2221) in paragraph at lines 12889--12898 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s [188] [189] [190] [191] Underfull \hbox (badness 2253) in paragraph at lines 13141--13143 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 13256--13258 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 13406--13408 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 13514--13518 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13525--13528 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . [198] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13566--13566 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [199] Underfull \hbox (badness 10000) in paragraph at lines 13658--13661 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13668--13668 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [200] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13756--13756 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, [201] Underfull \hbox (badness 7238) in paragraph at lines 13780--13787 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13780--13787 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 13780--13787 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- Underfull \hbox (badness 3965) in paragraph at lines 13788--13792 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [202] [203] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13951--13951 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 13952--13952 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 14031--14035 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14031--14035 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [206] [207] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14179--14179 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14182--14182 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [208] Underfull \hbox (badness 1168) in paragraph at lines 14266--14270 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14266--14270 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [209] Underfull \hbox (badness 6944) in paragraph at lines 14361--14364 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [210] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14386--14386 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 14520--14522 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14539--14539 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14541--14541 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14544--14544 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14550--14553 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 4254) in paragraph at lines 14566--14574 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14581--14585 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [213] Underfull \hbox (badness 10000) in paragraph at lines 14650--14652 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so [214] Underfull \hbox (badness 10000) in paragraph at lines 14656--14660 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, Underfull \hbox (badness 10000) in paragraph at lines 14656--14660 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14661--14669 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or Underfull \hbox (badness 3601) in paragraph at lines 14695--14699 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 14695--14699 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [215] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14762--14762 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [216] Overfull \hbox (25.98041pt too wide) in paragraph at lines 14784--14784 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2418) in paragraph at lines 15705--15709 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 15712--15715 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 15740--15747 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [230] [231] [232] [233] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15986--15986 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16011--16018 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [234] [235] [236] [237] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16279--16279 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16308--16308 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [238] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16359--16359 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16365--16369 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16365--16369 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [239] [240] [241] [242] [243] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16718--16718 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [244] [245] [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16968--16968 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [247] [248] [249] [250] Underfull \hbox (badness 2435) in paragraph at lines 17229--17231 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [251] Underfull \hbox (badness 1867) in paragraph at lines 17271--17278 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17271--17278 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17271--17278 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17286--17288 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17294--17294 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17304--17304 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [252] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17324--17324 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [253] [254] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17458--17458 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17464--17464 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17467--17467 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17473--17473 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [255] [256] [257] [258] [259] Underfull \hbox (badness 10000) in paragraph at lines 17812--17814 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [260] Underfull \hbox (badness 4217) in paragraph at lines 17896--17905 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 17911--17927 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 4699) in paragraph at lines 18325--18328 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [267] [268] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18448--18448 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [269] [270] Underfull \hbox (badness 4739) in paragraph at lines 18583--18585 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [271] [272] [273] [274] [275] [276] [277] Underfull \hbox (badness 1430) in paragraph at lines 18996--19001 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 18996--19001 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [278] Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19057--19062 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19057--19062 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [279] Underfull \hbox (badness 10000) in paragraph at lines 19117--19124 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19117--19124 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19117--19124 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19117--19124 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19133--19135 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [280] Underfull \hbox (badness 1975) in paragraph at lines 19205--19208 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [281] [282] [283] [284] [285] [286] Underfull \hbox (badness 1077) in paragraph at lines 19600--19605 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [287] Underfull \hbox (badness 10000) in paragraph at lines 19614--19621 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [288] Underfull \hbox (badness 10000) in paragraph at lines 19688--19692 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [289] Underfull \hbox (badness 10000) in paragraph at lines 19818--19822 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 19818--19822 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self [290] [291] Underfull \hbox (badness 10000) in paragraph at lines 19916--19923 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [292] [293] Underfull \hbox (badness 10000) in paragraph at lines 20037--20041 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [294] Underfull \hbox (badness 5161) in paragraph at lines 20092--20097 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20092--20097 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [295] [296] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20259--20259 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20263--20263 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [297] Underfull \hbox (badness 3343) in paragraph at lines 20319--20323 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [298] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20405--20405 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20416--20416 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [299] [300] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20525--20525 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (85.38034pt too wide) in paragraph at lines 20528--20528 []\T1/pcr/m/n/9 attach("all.RData") # safer and will warn about masked objects w/ same name in .GlobalEnv[] [301] Underfull \hbox (badness 6380) in paragraph at lines 20572--20577 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20630--20637 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20630--20637 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20630--20637 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [302] Underfull \hbox (badness 2564) in paragraph at lines 20650--20653 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 20680--20680 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [303] Underfull \hbox (badness 1205) in paragraph at lines 20703--20708 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [304] [305] [306] [307] Underfull \hbox (badness 2469) in paragraph at lines 21013--21019 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 1939) in paragraph at lines 21013--21019 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing names. Underfull \hbox (badness 10000) in paragraph at lines 21013--21019 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [308] [309] [310] [311] Underfull \hbox (badness 10000) in paragraph at lines 21327--21329 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [312] [313] [314] [315] [316] Overfull \hbox (52.98038pt too wide) in paragraph at lines 21631--21631 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 21632--21632 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21635--21635 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [317] [318] Underfull \hbox (badness 1655) in paragraph at lines 21759--21763 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [319] [320] [321] [322] Underfull \hbox (badness 2277) in paragraph at lines 22008--22011 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [323] [324] [325] [326] [327] [328] [329] Underfull \hbox (badness 10000) in paragraph at lines 22491--22497 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22491--22497 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins [330] Underfull \hbox (badness 1484) in paragraph at lines 22523--22531 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 2951) in paragraph at lines 22523--22531 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22523--22531 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [331] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22600--22600 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [332] Underfull \hbox (badness 10000) in paragraph at lines 22651--22655 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 22651--22655 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 10000) in paragraph at lines 23091--23099 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; [339] Underfull \hbox (badness 3849) in paragraph at lines 23205--23210 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [340] Underfull \hbox (badness 7308) in paragraph at lines 23282--23288 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5077) in paragraph at lines 23282--23288 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23292--23295 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23292--23295 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [341] [342] [343] Underfull \hbox (badness 10000) in paragraph at lines 23444--23446 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] Underfull \hbox (badness 2197) in paragraph at lines 24122--24126 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24122--24126 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24136--24140 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24136--24140 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to [354] Underfull \hbox (badness 10000) in paragraph at lines 24229--24235 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 24229--24235 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 24242--24244 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [355] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24293--24293 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [356] [357] [358] Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24486--24492 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [359] Underfull \hbox (badness 4120) in paragraph at lines 24572--24579 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [360] [361] Underfull \hbox (badness 1694) in paragraph at lines 24708--24711 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [362] [363] [364] [365] Underfull \hbox (badness 1603) in paragraph at lines 24947--24949 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [366] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25065--25073 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [367] [368] Underfull \hbox (badness 5475) in paragraph at lines 25202--25212 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25244--25247 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25259--25261 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [369] [370] [371] Underfull \hbox (badness 3138) in paragraph at lines 25518--25524 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25518--25524 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 25518--25524 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 25531--25534 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 25555--25557 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25567--25571 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25567--25571 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is [372] Underfull \hbox (badness 10000) in paragraph at lines 25572--25578 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 25587--25592 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 25593--25604 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 25605--25608 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25615--25627 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 25615--25627 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a Underfull \hbox (badness 10000) in paragraph at lines 25629--25636 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25629--25636 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25629--25636 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 25629--25636 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [373] [374] [375] [376] [377] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25963--25963 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 25976--25980 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25976--25980 \T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.y)] [378] [379] [380] [381] [382] Underfull \hbox (badness 4341) in paragraph at lines 26299--26301 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26335--26341 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*, collapse=", ")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with [383] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26357--26357 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26369--26369 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [384] [385] [386] [387] [388] [389] [390] Underfull \hbox (badness 10000) in paragraph at lines 26802--26806 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [391] Underfull \hbox (badness 1796) in paragraph at lines 26865--26868 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 27060--27063 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [395] [396] [397] [398] [399] [400] [401] [402] [403] Underfull \hbox (badness 1226) in paragraph at lines 27692--27697 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [404] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27737--27737 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [405] [406] [407] [408] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28003--28003 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28014--28014 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28020--28020 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28021--28021 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28024--28024 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [409] Underfull \hbox (badness 7415) in paragraph at lines 28099--28103 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [410] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28120--28120 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [411] Underfull \hbox (badness 2418) in paragraph at lines 28268--28279 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [412] [413] Underfull \hbox (badness 1248) in paragraph at lines 28392--28399 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 28392--28399 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [414] Underfull \hbox (badness 1533) in paragraph at lines 28501--28504 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [415] [416] Underfull \hbox (badness 1337) in paragraph at lines 28598--28601 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [417] Overfull \hbox (42.78088pt too wide) in paragraph at lines 28646--28646 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 28663--28674 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in Underfull \hbox (badness 10000) in paragraph at lines 28675--28678 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [418] [419] Underfull \hbox (badness 1117) in paragraph at lines 28770--28776 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [420] [421] [422] [423] [424] [425] Underfull \hbox (badness 4048) in paragraph at lines 29148--29153 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29148--29153 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29148--29153 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [426] [427] [428] [429] [430] [431] [432] [433] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29686--29686 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [434] [435] [436] [437] Overfull \hbox (13.9408pt too wide) in paragraph at lines 29970--29972 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [438] [439] Underfull \hbox (badness 7558) in paragraph at lines 30186--30190 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 30196--30198 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the [440] Underfull \hbox (badness 5417) in paragraph at lines 30201--30204 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30205--30207 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30208--30210 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 10000) in paragraph at lines 30615--30619 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31300--31300 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 31431--31435 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31431--31435 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [459] [460] [461] Underfull \hbox (badness 2302) in paragraph at lines 31671--31678 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31671--31678 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [462] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31723--31723 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [463] Underfull \hbox (badness 1158) in paragraph at lines 31827--31832 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [464] Underfull \hbox (badness 10000) in paragraph at lines 31854--31860 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 31854--31860 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [465] Underfull \hbox (badness 10000) in paragraph at lines 31930--31935 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 31930--31935 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [466] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32012--32012 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [467] [468] [469] Underfull \hbox (badness 2809) in paragraph at lines 32276--32282 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32283--32286 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1735) in paragraph at lines 33087--33093 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [482] Underfull \hbox (badness 4303) in paragraph at lines 33103--33106 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [483] [484] [485] [486] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33421--33421 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [487] [488] [489] [490] Overfull \hbox (6.78088pt too wide) in paragraph at lines 33670--33670 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 33672--33672 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 10000) in paragraph at lines 33715--33721 [][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/ m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/ 10 , see Underfull \hbox (badness 10000) in paragraph at lines 33715--33721 \T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T 1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard- Underfull \hbox (badness 10000) in paragraph at lines 33715--33721 \T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i s the de-fault cur-rently; [491] Underfull \hbox (badness 2512) in paragraph at lines 33730--33732 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [492] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33826--33826 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:[] [493] [494] [495] [496] [497] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34154--34154 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34169--34169 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [498] [499] [500] [501] [502] [503] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34608--34608 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 34609--34609 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [504] [505] [506] [507] Overfull \hbox (63.78036pt too wide) in paragraph at lines 34873--34873 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [508] Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 34957--34967 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 34957--34967 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [509] Underfull \hbox (badness 10000) in paragraph at lines 35001--35007 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35001--35007 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 35001--35007 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35013--35020 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35013--35020 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35013--35020 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [510] [511] [512] [513] [514] Underfull \hbox (badness 10000) in paragraph at lines 35311--35317 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [515] [516] Underfull \hbox (badness 1163) in paragraph at lines 35499--35506 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 35499--35506 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [517] [518] [519] [520] Underfull \hbox (badness 1142) in paragraph at lines 35762--35768 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 35777--35777 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [521] [522] [523] [524] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36025--36025 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [525] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36069--36069 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [526] [527] [528] [529] [530] [531] Overfull \hbox (52.98038pt too wide) in paragraph at lines 36501--36501 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 36504--36504 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [532] Underfull \hbox (badness 10000) in paragraph at lines 36555--36562 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 36555--36562 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [533] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36606--36606 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [534] [535] [536] Underfull \hbox (badness 2762) in paragraph at lines 36841--36850 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 36841--36850 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [537] Overfull \hbox (31.3804pt too wide) in paragraph at lines 36903--36903 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [538] Underfull \vbox (badness 7777) has occurred while \output is active [539] [540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37068--37068 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [541] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37106--37106 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 3219) in paragraph at lines 37155--37160 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37155--37160 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [542] Underfull \hbox (badness 2452) in paragraph at lines 37245--37248 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37245--37248 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 37432--37436 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 37447--37450 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [546] [547] [548] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37640--37640 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [549] [550] [551] Underfull \hbox (badness 1082) in paragraph at lines 37778--37781 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [552] [553] Underfull \hbox (badness 1038) in paragraph at lines 37965--37968 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [554] [555] [556] [557] [558] Underfull \hbox (badness 1515) in paragraph at lines 38304--38307 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [559] [560] [561] Underfull \hbox (badness 4096) in paragraph at lines 38529--38532 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 38643--38647 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [564] [565] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38794--38794 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 38796--38796 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 38798--38798 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] [566] Underfull \hbox (badness 10000) in paragraph at lines 38811--38813 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [567] Underfull \hbox (badness 10000) in paragraph at lines 38891--38894 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [568] [569] Underfull \hbox (badness 1867) in paragraph at lines 39009--39013 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39071--39075 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1371) in paragraph at lines 39431--39435 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 TZ \T1/ptm/m/n/10 is set but empty or in-val id, most plat-forms de-fault to `\T1/pcr/m/n/10 UTC\T1/ptm/m/n/10 ', the time z one col- Underfull \hbox (badness 1648) in paragraph at lines 39431--39435 \T1/ptm/m/n/10 lo-qui-ally known as `\T1/pcr/m/n/10 GMT\T1/ptm/m/n/10 ' (see [] []$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Coordinated _ [576] Underfull \hbox (badness 5637) in paragraph at lines 39504--39513 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the Ol-son/IANA Underfull \hbox (badness 1629) in paragraph at lines 39504--39513 \T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion in the file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 39514--39521 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 39514--39521 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 39514--39521 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [577] [578] [579] [580] Underfull \hbox (badness 10000) in paragraph at lines 39798--39800 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [581] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39920--39920 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39922--39922 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [582] [583] [584] [585] [586] Underfull \hbox (badness 6542) in paragraph at lines 40258--40260 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [587] [588] [589] Underfull \hbox (badness 3460) in paragraph at lines 40424--40427 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 40431--40439 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 40431--40439 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less Underfull \hbox (badness 10000) in paragraph at lines 40440--40444 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 40440--40444 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 40440--40444 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 40461--40466 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [590] Underfull \hbox (badness 3895) in paragraph at lines 40523--40535 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 40523--40535 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [591] [592] [593] Underfull \hbox (badness 10000) in paragraph at lines 40708--40711 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [594] [595] Overfull \hbox (9.78043pt too wide) in paragraph at lines 40845--40845 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [596] [597] [598] [599] [600] [601] [602] Underfull \hbox (badness 1803) in paragraph at lines 41396--41399 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), [603] Underfull \hbox (badness 2334) in paragraph at lines 41400--41407 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 4726) in paragraph at lines 41426--41430 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 41426--41430 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [604] [605] [606] Underfull \hbox (badness 3668) in paragraph at lines 41615--41617 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [607] [608] [609] [610] Underfull \hbox (badness 6220) in paragraph at lines 41897--41902 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 41897--41902 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 41897--41902 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 41913--41918 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 1603) in paragraph at lines 41932--41936 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [611] Underfull \hbox (badness 10000) in paragraph at lines 41997--42000 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 41997--42000 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42003--42009 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and [612] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42038--42038 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [613] Underfull \hbox (badness 1622) in paragraph at lines 42116--42118 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [614] [615] [616] [617] Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 42378--42383 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [618] Underfull \hbox (badness 2846) in paragraph at lines 42470--42474 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42510--42510 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 42531--42535 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [620]) (./compiler-pkg.tex Chapter 2. [621] [622] [623] [624]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [625] [626] [627] [628] [629] Overfull \hbox (15.18042pt too wide) in paragraph at lines 294--294 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [630] Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [631] [632] [633] [634] [635] Overfull \hbox (66.81013pt too wide) in paragraph at lines 691--694 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [636] [637] Overfull \hbox (66.81013pt too wide) in paragraph at lines 824--827 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [638] [639] [640] [641] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [642] [643] [644] [645] [646] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 1525--1528 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1525--1528 \T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m /n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a bove [649] Underfull \hbox (badness 1325) in paragraph at lines 1606--1611 []\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [650] [651] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1713--1716 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [652] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1815--1815 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [653] [654] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1931--1931 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1932--1932 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [655] [656] [657] [658] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2135--2138 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [659] [660] [661] [662] [663] [664] [665] [666] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2676--2679 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [667] Overfull \vbox (13.87083pt too high) has occurred while \output is active [668] Underfull \vbox (badness 1789) has occurred while \output is active [669] [670] Overfull \vbox (12.25539pt too high) has occurred while \output is active [671] [672] Overfull \vbox (17.12102pt too high) has occurred while \output is active [673] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3105--3105 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [674] [675] [676] [677] [678] [679] [680] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3562--3562 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [681] [682] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3710--3713 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [683] Overfull \vbox (10.49593pt too high) has occurred while \output is active [684] Underfull \hbox (badness 1173) in paragraph at lines 3844--3848 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [685] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3919--3919 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3948--3951 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699]) (./grDevices-pkg.tex [700] Chapter 4. [701] [702] [703] [704] [705] [706] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [707] Overfull \hbox (6.78088pt too wide) in paragraph at lines 470--470 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [708] [709] [710] [711] [712] [713] [714] [715] [716] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [717] Underfull \hbox (badness 1325) in paragraph at lines 1131--1137 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [718] Underfull \hbox (badness 10000) in paragraph at lines 1172--1174 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [719] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1224--1224 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [720] Underfull \hbox (badness 1173) in paragraph at lines 1266--1269 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [721] [722] [723] Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1481--1485 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1526--1529 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [724] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [725] [726] [727] Underfull \hbox (badness 1565) in paragraph at lines 1754--1759 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1754--1759 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [728] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1837--1837 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [729] Underfull \hbox (badness 1184) in paragraph at lines 1878--1888 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1878--1888 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [731] [732] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [733] [734] Underfull \hbox (badness 2326) in paragraph at lines 2254--2264 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2254--2264 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2254--2264 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2254--2264 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [735] [736] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2357--2357 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [737] [738] [739] [740] [741] [742] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [743] [744] [745] [746] [747] [748] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3138--3138 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3139--3139 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3170--3172 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [749] Underfull \hbox (badness 10000) in paragraph at lines 3230--3235 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [750] [751] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3382--3382 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [752] [753] Underfull \hbox (badness 3525) in paragraph at lines 3489--3492 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 1968) in paragraph at lines 3503--3505 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [754] [755] [756] [757] Underfull \hbox (badness 5939) in paragraph at lines 3797--3802 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [758] [759] [760] [761] [762] [763] Underfull \hbox (badness 7576) in paragraph at lines 4170--4177 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4170--4177 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [764] [765] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4287--4287 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] Underfull \hbox (badness 1502) in paragraph at lines 4334--4339 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [766] [767] Underfull \hbox (badness 4765) in paragraph at lines 4493--4495 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if [768] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4507--4507 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 5077) in paragraph at lines 4547--4553 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [769] Underfull \hbox (badness 1342) in paragraph at lines 4563--4565 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [770] Underfull \hbox (badness 1874) in paragraph at lines 4640--4648 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [771] Underfull \hbox (badness 1755) in paragraph at lines 4707--4709 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [772] [773] Underfull \hbox (badness 7344) in paragraph at lines 4878--4880 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4889--4893 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [774] [775] Underfull \hbox (badness 1552) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5002--5011 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5012--5014 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5044--5050 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [776] Underfull \hbox (badness 10000) in paragraph at lines 5070--5077 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [777] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5171--5171 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [778] [779] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5283--5283 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5289--5293 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [780] Underfull \hbox (badness 10000) in paragraph at lines 5369--5371 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [781] Underfull \hbox (badness 1072) in paragraph at lines 5405--5411 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [782] [783] [784] [785] [786] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5728--5728 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5741--5744 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 1189) in paragraph at lines 6138--6140 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 6236--6238 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6275--6282 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 6275--6282 \T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s ys-tems which have the Wine [795] Underfull \hbox (badness 3088) in paragraph at lines 6359--6363 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [796] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6404--6404 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] Underfull \hbox (badness 10000) in paragraph at lines 6436--6439 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [797] [798] Underfull \hbox (badness 5637) in paragraph at lines 6527--6533 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6560--6563 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [799] [800] [801] Underfull \hbox (badness 6157) in paragraph at lines 6717--6720 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6728--6730 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [802] [803] [804]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [805] [806] [807] [808] Underfull \hbox (badness 1412) in paragraph at lines 286--291 []\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [809] [810] [811] Underfull \hbox (badness 2726) in paragraph at lines 465--471 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [812] [813] [814] Underfull \hbox (badness 10000) in paragraph at lines 655--659 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 655--659 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if Underfull \hbox (badness 2735) in paragraph at lines 683--690 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [815] Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [816] [817] Underfull \hbox (badness 1062) in paragraph at lines 849--852 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [818] [819] [820] [821] [822] [823] [824] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1283--1283 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [825] Underfull \hbox (badness 1024) in paragraph at lines 1328--1336 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1356--1362 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1356--1362 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1362--1364 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1384--1388 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [826] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1432--1432 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1433--1433 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1440--1440 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [827] [828] [829] [830] [831] Underfull \hbox (badness 10000) in paragraph at lines 1740--1746 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [832] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1786--1786 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [833] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1869--1869 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [834] [835] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1998--1998 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2003--2003 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [836] [837] [838] [839] [840] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [841] [842] [843] [844] [845] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2617--2617 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [846] [847] Underfull \hbox (badness 5878) in paragraph at lines 2778--2782 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2803--2806 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [848] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2831--2831 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2835--2835 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [849] Underfull \hbox (badness 10000) in paragraph at lines 2887--2890 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [850] [851] [852] [853] Underfull \hbox (badness 1755) in paragraph at lines 3148--3152 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [854] Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3223--3228 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [855] [856] [857] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3406--3406 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3425--3425 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3429--3429 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [858] [859] [860] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3606--3606 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3607--3607 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3644--3644 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [861] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3696--3696 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Underfull \vbox (badness 10000) has occurred while \output is active [862] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3716--3716 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3779--3783 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for [863] [864] [865] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [866] [867] Underfull \hbox (badness 3930) in paragraph at lines 4094--4096 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [868] [869] [870] [871] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [872] Underfull \hbox (badness 1286) in paragraph at lines 4402--4405 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4500--4500 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor)[] [874] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4504--4504 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [875] Underfull \hbox (badness 1264) in paragraph at lines 4622--4635 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [876] [877] Underfull \hbox (badness 7925) in paragraph at lines 4759--4765 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. [878] [879] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [880 ] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 [881 ] [882] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [883] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5197--5197 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5198--5198 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [884] [885] Underfull \hbox (badness 3954) in paragraph at lines 5299--5302 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5355--5359 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [886] [887] [888] [889] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5563--5563 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5564--5564 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5615--5619 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., Underfull \hbox (badness 1024) in paragraph at lines 5615--5619 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [890] [891] [892] [893] [894] [895] [896] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6048--6048 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [897] [898] [899] [900] [901] [902] Underfull \hbox (badness 10000) in paragraph at lines 6475--6477 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [903] [904] Underfull \hbox (badness 1028) in paragraph at lines 6569--6571 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [905 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6706--6706 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [906] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6737--6737 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] Underfull \hbox (badness 10000) in paragraph at lines 6859--6861 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6886--6886 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6892--6892 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [909] Underfull \hbox (badness 2600) in paragraph at lines 6952--6954 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [910] [911] [912] Underfull \hbox (badness 1881) in paragraph at lines 7141--7146 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7184--7184 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [914] [915] [916] [917] [918] [919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7571--7571 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7575--7575 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [920] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7587--7587 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [921] [922] [923] [924] [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7930--7930 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [926] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7937--7937 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [927] [928] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8108--8108 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8109--8109 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [929] [930] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8213--8213 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8224--8229 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [931] [932] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8328--8328 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8343--8343 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [933] [934] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [935] [936] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8647--8647 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [937] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8709--8715 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [938]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [939] Underfull \hbox (badness 1205) in paragraph at lines 8822--8824 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [940] [941] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8941--8941 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [942]) (./grid-pkg.tex Chapter 6. [943] [944] [945] [946] [947] [948] Underfull \hbox (badness 10000) in paragraph at lines 383--389 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 383--389 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1023--1023 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [959] Underfull \hbox (badness 1430) in paragraph at lines 1072--1077 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [960] [961] [962] Underfull \hbox (badness 3219) in paragraph at lines 1286--1289 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [963] [964] [965] [966] [967] [968] [969] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1673--1673 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [970] [971] [972] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1888--1888 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [973] Underfull \hbox (badness 2961) in paragraph at lines 1924--1929 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [974] Underfull \hbox (badness 1430) in paragraph at lines 1983--1988 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2012--2015 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [975] [976] [977] Underfull \hbox (badness 2894) in paragraph at lines 2219--2226 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [978] [979] [980] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2375--2375 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2387--2392 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [981] [982] [983] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2580--2580 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2612--2612 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [984] [985] [986] [987] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2852--2852 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [988] [989] [990] [991] [992] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3162--3162 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [993] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3258--3258 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [994] Underfull \hbox (badness 2799) in paragraph at lines 3292--3298 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [995] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3384--3384 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [996] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3391--3391 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [997] [998] [999] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3600--3600 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 1430) in paragraph at lines 4157--4162 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1009] [1010] [1011] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1012] Underfull \hbox (badness 1430) in paragraph at lines 4386--4391 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1013] [1014] [1015] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] Underfull \hbox (badness 10000) in paragraph at lines 5174--5176 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] Underfull \hbox (badness 3449) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1036] [1037] [1038] [1039] [1040] Underfull \hbox (badness 1867) in paragraph at lines 6172--6174 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 6209--6215 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1041] [1042] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1043] [1044] [1045] [1046] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6545--6545 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1047]) (./methods-pkg.tex [1048] Chapter 7. [1049] [1050] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1051] [1052] [1053] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1054] [1055] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1056] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1057] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1058] [1059] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1795--1795 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1797--1797 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1839--1841 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1073] [1074] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1075] [1076] [1077] Underfull \hbox (badness 1132) in paragraph at lines 2215--2220 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1078] [1079] Underfull \hbox (badness 10000) in paragraph at lines 2329--2333 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2361--2361 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1080] [1081] [1082] Underfull \hbox (badness 3792) in paragraph at lines 2575--2578 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2606--2610 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1083] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2662--2662 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1084] [1085] [1086] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2881--2881 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1087] [1088] [1089] [1090] [1091] [1092] [1093] Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3404--3409 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1094] [1095] Underfull \hbox (badness 10000) in paragraph at lines 3532--3536 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1096] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3645--3654 [] [1097] [1098] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3765--3766 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 Underfull \hbox (badness 10000) in paragraph at lines 3812--3813 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1099] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3831--3832 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") Overfull \hbox (120.78088pt too wide) in paragraph at lines 3849--3850 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3911--3915 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 4138--4140 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1103] [1104] Underfull \hbox (badness 1629) in paragraph at lines 4250--4259 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4311--4311 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4312--4312 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4369--4369 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1107] [1108] Underfull \hbox (badness 1033) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1109] Underfull \hbox (badness 2126) in paragraph at lines 4577--4585 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1110] [1111] [1112] Underfull \hbox (badness 10000) in paragraph at lines 4814--4823 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1113] [1114] [1115] [1116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5198--5198 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1117] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5226--5226 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5240--5240 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1118] [1119] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1120] Underfull \hbox (badness 10000) in paragraph at lines 5466--5468 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1121] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1122] [1123] [1124] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1125] Underfull \hbox (badness 10000) in paragraph at lines 5760--5764 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5760--5764 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1126] Underfull \hbox (badness 10000) in paragraph at lines 5851--5855 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5851--5855 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1127] [1128] [1129] [1130] Underfull \hbox (badness 10000) in paragraph at lines 6213--6229 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1131] [1132] Underfull \hbox (badness 1248) in paragraph at lines 6346--6350 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6346--6350 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1133] Underfull \hbox (badness 4647) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1134] Underfull \hbox (badness 1072) in paragraph at lines 6578--6585 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1135] Underfull \hbox (badness 2875) in paragraph at lines 6650--6659 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6650--6659 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1136] Underfull \vbox (badness 10000) has occurred while \output is active [1137] [1138] [1139]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1140] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7012--7012 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7068--7075 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1141] [1142] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7203--7203 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1143]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1144] Underfull \hbox (badness 6708) in paragraph at lines 7312--7324 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7312--7324 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7312--7324 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1145] [1146] Underfull \hbox (badness 1694) in paragraph at lines 7475--7477 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7499--7502 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1147] [1148] Underfull \hbox (badness 10000) in paragraph at lines 7666--7673 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7666--7673 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7666--7673 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] Underfull \hbox (badness 1052) in paragraph at lines 8492--8499 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1160] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8625--8625 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1161] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8700--8700 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1162] [1163] [1164] [1165] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1166] [1167] [1168] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9170--9170 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1169] [1170] Underfull \vbox (badness 2277) has occurred while \output is active [1171] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9432--9432 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1172] [1173] [1174] [1175] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9740--9740 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1176] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9850--9850 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1177] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9861--9861 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] Underfull \hbox (badness 10000) in paragraph at lines 10559--10561 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10567--10571 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1187] [1188] [1189] [1190]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1191] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1192] [1193] Underfull \hbox (badness 1024) in paragraph at lines 196--199 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1194] Underfull \hbox (badness 10000) in paragraph at lines 287--290 []\T1/ptm/m/n/10 Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.3.0 the de-fault wa s \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/10 ex-cept on Win-dows, but Underfull \hbox (badness 10000) in paragraph at lines 305--313 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1195] [1196] Underfull \hbox (badness 10000) in paragraph at lines 423--425 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1197] [1198] [1199] [1200] Underfull \hbox (badness 1917) in paragraph at lines 718--727 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 718--727 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1201] [1202] Underfull \hbox (badness 10000) in paragraph at lines 855--858 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1203] [1204] [1205] Underfull \hbox (badness 5388) in paragraph at lines 1048--1053 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from [1206] Underfull \hbox (badness 10000) in paragraph at lines 1072--1080 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1109--1109 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1207] [1208] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1225--1225 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1268--1271 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1209] Underfull \hbox (badness 3375) in paragraph at lines 1314--1316 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1210] [1211]) (./splines-pkg.tex [1212] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1213] [1214] [1215] [1216] [1217] [1218] [1219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1220] [1221] [1222] [1223] Overfull \hbox (25.98041pt too wide) in paragraph at lines 699--699 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1224] [1225] [1226]) (./stats-pkg.tex Chapter 10. [1227] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1228] [1229] [1230] [1231] [1232] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1233] [1234] [1235] [1236] [1237] [1238] [1239] Underfull \hbox (badness 1024) in paragraph at lines 848--850 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] Underfull \hbox (badness 10000) in paragraph at lines 1392--1394 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1248] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] Underfull \hbox (badness 10000) in paragraph at lines 2081--2086 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2081--2086 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2081--2086 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2087--2093 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2087--2093 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1258] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1259] [1260] [1261] [1262] Underfull \hbox (badness 1221) in paragraph at lines 2433--2438 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2433--2438 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1263] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1264] [1265] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2645--2645 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1266] [1267] [1268] [1269] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2885--2885 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1270] [1271] [1272] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3093--3095 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1273] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3140--3140 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3141--3141 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1274] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1275] [1276] [1277] [1278] [1279] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3531--3531 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1280] [1281] [1282] [1283] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3801--3801 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1284] [1285] [1286] [1287] [1288] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4086--4086 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4087--4087 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1289] [1290] [1291] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4322--4322 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1292] [1293] [1294] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4490--4490 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1295] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1296] [1297] [1298] [1299] [1300] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4942--4942 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4944--4944 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1301] [1302] Underfull \hbox (badness 7397) in paragraph at lines 5031--5035 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5031--5035 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1303] [1304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5165--5165 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5183--5183 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5210--5212 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by Underfull \hbox (badness 10000) in paragraph at lines 5215--5217 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1305] [1306] [1307] Underfull \hbox (badness 1436) in paragraph at lines 5393--5398 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5393--5398 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5393--5398 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1308] [1309] [1310] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5588--5588 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1311] Underfull \hbox (badness 1168) in paragraph at lines 5660--5665 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1312] [1313] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5754--5754 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1314] [1315] [1316] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5939--5939 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1317] [1318] Underfull \hbox (badness 10000) in paragraph at lines 6102--6107 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When [1319] [1320] [1321] Underfull \hbox (badness 5954) in paragraph at lines 6298--6300 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1322] Underfull \hbox (badness 2503) in paragraph at lines 6380--6383 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6384--6386 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6387--6392 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1323] Underfull \hbox (badness 7238) in paragraph at lines 6423--6426 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1324] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6458--6458 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6473--6473 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6488--6488 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1325] [1326] [1327] [1328] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6730--6730 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1329] [1330] Underfull \vbox (badness 10000) has occurred while \output is active [1331] [1332] [1333] [1334] Underfull \hbox (badness 10000) in paragraph at lines 7128--7132 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1335] Underfull \hbox (badness 6493) in paragraph at lines 7225--7228 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1336] [1337] Underfull \hbox (badness 10000) in paragraph at lines 7362--7365 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 10000) in paragraph at lines 7772--7777 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1344] [1345] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7910--7912 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1346] [1347] [1348] Underfull \hbox (badness 1210) in paragraph at lines 8127--8129 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1349] [1350] [1351] [1352] [1353] [1354] [1355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571 [] \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino mial()$mu_eta[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8593--8593 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8596--8596 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1356] [1357] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8734--8734 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1358] Underfull \hbox (badness 1859) in paragraph at lines 8773--8778 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1359] [1360] [1361] [1362] [1363] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9141--9141 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate S", "VeryS")))[] [1364] [1365] [1366] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2443) in paragraph at lines 9761--9767 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1373] [1374] [1375] Underfull \hbox (badness 3758) in paragraph at lines 9974--9977 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1376] [1377] [1378] [1379] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1380] Underfull \hbox (badness 4132) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1381] Underfull \hbox (badness 10000) in paragraph at lines 10377--10380 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1382] [1383] [1384] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1385] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1386] Underfull \hbox (badness 10000) in paragraph at lines 10700--10706 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10738--10743 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1387] [1388] Underfull \hbox (badness 2635) in paragraph at lines 10871--10874 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1389] [1390] [1391] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11073--11082 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1392] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11155--11155 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1393] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11188--11188 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11201--11205 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1394] [1395] [1396] Underfull \hbox (badness 7379) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1397] [1398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1399] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11587--11587 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11599--11599 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1400] Underfull \hbox (badness 1062) in paragraph at lines 11648--11653 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11665--11667 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1401] [1402] Underfull \hbox (badness 3623) in paragraph at lines 11816--11818 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1403] [1404] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11912--11912 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1405] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12005--12005 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1406] Underfull \hbox (badness 10000) in paragraph at lines 12053--12056 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1407] [1408] [1409] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1410] [1411] Underfull \hbox (badness 2753) in paragraph at lines 12345--12347 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1412] [1413] Underfull \hbox (badness 1292) in paragraph at lines 12470--12474 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1414] Underfull \hbox (badness 10000) in paragraph at lines 12583--12585 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12589--12593 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] Underfull \hbox (badness 4518) in paragraph at lines 13284--13289 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1426] [1427] [1428] Underfull \hbox (badness 10000) in paragraph at lines 13478--13482 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1429] [1430] Underfull \hbox (badness 6995) in paragraph at lines 13663--13665 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1431] [1432] [1433] Underfull \hbox (badness 1163) in paragraph at lines 13811--13819 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1434] Underfull \hbox (badness 4518) in paragraph at lines 13931--13936 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1435] [1436] Underfull \hbox (badness 10000) in paragraph at lines 14069--14073 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14069--14073 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1437] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14117--14117 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14118--14118 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1438] Underfull \hbox (badness 10000) in paragraph at lines 14173--14176 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14173--14176 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1439] [1440] [1441] [1442] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14459--14459 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14460--14460 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1443] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14510--14512 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14553--14553 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1444] [1445] [1446] [1447] [1448] [1449] [1450] Underfull \hbox (badness 2726) in paragraph at lines 14956--14959 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15671--15671 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1462] [1463] Underfull \hbox (badness 1014) in paragraph at lines 15809--15814 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1464] Underfull \hbox (badness 1648) in paragraph at lines 15869--15871 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 15883--15892 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 15883--15892 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1465] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15951--15951 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16504--16504 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1475] [1476] [1477] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16732--16732 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2772) in paragraph at lines 17167--17170 []\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate s. When Underfull \hbox (badness 10000) in paragraph at lines 17167--17170 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr /m/n/10 start \T1/ptm/m/n/10 is tried (if [1485] [1486] Underfull \hbox (badness 2359) in paragraph at lines 17287--17289 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1487] Underfull \vbox (badness 10000) has occurred while \output is active [1488] Underfull \vbox (badness 10000) has occurred while \output is active [1489] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17459--17459 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1490] Underfull \hbox (badness 10000) in paragraph at lines 17539--17543 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1491] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17619--17619 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1492] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17666--17666 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17713--17713 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Underfull \hbox (badness 1248) in paragraph at lines 18203--18206 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1127) in paragraph at lines 18216--18220 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1501] Underfull \hbox (badness 1478) in paragraph at lines 18224--18228 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and Underfull \hbox (badness 2042) in paragraph at lines 18277--18279 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1502] [1503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18373--18373 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1504] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18415--18415 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18448--18448 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18451--18451 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1505] Underfull \hbox (badness 2564) in paragraph at lines 18486--18497 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18486--18497 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1506] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18549--18549 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1507] [1508] [1509] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18764--18764 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1510] Underfull \hbox (badness 1337) in paragraph at lines 18840--18843 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1511] [1512] [1513] [1514] [1515] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19156--19156 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1516] [1517] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19244--19244 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19247--19247 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1518] Underfull \hbox (badness 3049) in paragraph at lines 19326--19330 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1519] [1520] [1521] [1522] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19569--19569 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19576--19578 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19579--19582 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1523] Underfull \hbox (badness 1107) in paragraph at lines 19637--19639 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1524] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19692--19692 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1525] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19699--19699 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] Underfull \hbox (badness 10000) in paragraph at lines 19749--19752 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 19749--19752 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1526] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19793--19793 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1527] [1528] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19918--19918 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1529] Underfull \hbox (badness 10000) in paragraph at lines 19981--19983 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1530] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20029--20029 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) Underfull \hbox (badness 10000) in paragraph at lines 20084--20086 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1531] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20121--20121 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] Overfull \hbox (25.98041pt too wide) in paragraph at lines 20951--20951 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1545] Underfull \hbox (badness 6859) in paragraph at lines 21018--21025 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21029--21035 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Overfull \hbox (78.78088pt too wide) in paragraph at lines 22044--22044 [] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) %in % c("Pr(", "p-v"),[] [1562] [1563] [1564] [1565] [1566] Underfull \hbox (badness 1337) in paragraph at lines 22367--22373 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Overfull \hbox (133.98029pt too wide) in paragraph at lines 22912--22912 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1575] [1576] [1577] Underfull \hbox (badness 1028) in paragraph at lines 23052--23055 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1578] Underfull \hbox (badness 10000) in paragraph at lines 23162--23165 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23162--23165 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1579] Underfull \hbox (badness 10000) in paragraph at lines 23217--23219 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1580] Underfull \hbox (badness 10000) in paragraph at lines 23279--23281 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1581] [1582] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23381--23381 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1583] [1584] [1585] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23601--23601 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1586] [1587] Underfull \hbox (badness 10000) in paragraph at lines 23747--23750 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1588] Underfull \hbox (badness 2134) in paragraph at lines 23798--23802 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 23811--23811 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1589] [1590] [1591] [1592] [1593] [1594] [1595] Underfull \hbox (badness 2591) in paragraph at lines 24268--24274 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][ ][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/ ptm/m/n/10 mod-els (with ex-am- [1596] [1597] [1598] Underfull \hbox (badness 1867) in paragraph at lines 24465--24467 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1599] Underfull \hbox (badness 10000) in paragraph at lines 24478--24482 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24478--24482 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Overfull \hbox (20.58041pt too wide) in paragraph at lines 24514--24514 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1600] [1601] [1602] Underfull \hbox (badness 2495) in paragraph at lines 24704--24713 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1603] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24786--24786 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 24793--24795 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1604] [1605] Overfull \hbox (25.98041pt too wide) in paragraph at lines 24880--24880 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 24905--24905 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 24908--24908 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1606] Underfull \hbox (badness 10000) in paragraph at lines 24950--24955 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 24950--24955 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1607] Underfull \hbox (badness 2980) in paragraph at lines 25095--25097 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1608] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25131--25131 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] [1609] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25180--25180 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Underfull \vbox (badness 10000) has occurred while \output is active [1610] [1611] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25303--25303 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1612] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25370--25370 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1613] [1614] [1615] [1616] [1617] [1618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 25746--25746 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 25799--25802 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1619] [1620] Overfull \hbox (31.3804pt too wide) in paragraph at lines 25925--25925 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 25926--25926 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1621] Underfull \hbox (badness 2922) in paragraph at lines 25992--25997 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1622] Underfull \hbox (badness 2922) in paragraph at lines 26054--26059 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 3240) in paragraph at lines 26066--26070 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff [1623] Underfull \hbox (badness 2922) in paragraph at lines 26111--26116 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1624] Underfull \hbox (badness 2922) in paragraph at lines 26172--26178 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1625] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26194--26194 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26210--26210 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1626] [1627] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26324--26324 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) Overfull \hbox (4.38043pt too wide) in paragraph at lines 26347--26347 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response and gradient[] [1628] Underfull \hbox (badness 2922) in paragraph at lines 26385--26390 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1629] Underfull \hbox (badness 2922) in paragraph at lines 26441--26446 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 2922) in paragraph at lines 26499--26504 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1630] Underfull \hbox (badness 2922) in paragraph at lines 26554--26559 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26575--26575 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Underfull \hbox (badness 6493) in paragraph at lines 26623--26628 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1632] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26649--26649 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26651--26651 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1633] [1634] [1635] [1636] [1637] [1638] [1639] Underfull \hbox (badness 10000) in paragraph at lines 27147--27150 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27147--27150 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1640] [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 3396) in paragraph at lines 27576--27578 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1647] [1648] [1649] Underfull \hbox (badness 2237) in paragraph at lines 27753--27755 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1650] [1651] Underfull \hbox (badness 2591) in paragraph at lines 27917--27919 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1652] Underfull \hbox (badness 2237) in paragraph at lines 27963--27966 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1653] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28036--28036 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1654] [1655] Underfull \hbox (badness 3407) in paragraph at lines 28144--28148 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1656] [1657] Underfull \hbox (badness 1337) in paragraph at lines 28277--28281 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1658] [1659] Underfull \hbox (badness 10000) in paragraph at lines 28394--28397 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1660] [1661] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28523--28523 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28551--28551 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1662] Underfull \hbox (badness 1616) in paragraph at lines 28577--28580 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1663] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28656--28656 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1664] Overfull \hbox (0.78088pt too wide) in paragraph at lines 28733--28733 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1665] Underfull \hbox (badness 5050) in paragraph at lines 28769--28774 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1666] Underfull \hbox (badness 2205) in paragraph at lines 28822--28827 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29417--29417 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1675] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29418--29418 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1676] [1677] [1678] [1679] Underfull \hbox (badness 10000) in paragraph at lines 29703--29707 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 29703--29707 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 29714--29714 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29715--29715 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1680] [1681] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29841--29841 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29850--29850 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] [1682] [1683] [1684] [1685] Underfull \hbox (badness 1337) in paragraph at lines 30067--30071 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] Underfull \hbox (badness 1337) in paragraph at lines 30551--30555 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1694] Underfull \hbox (badness 1946) in paragraph at lines 30628--30633 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 30650--30652 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1695] [1696] [1697] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30975--30975 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1700] Underfull \hbox (badness 6775) in paragraph at lines 31032--31037 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1701] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31095--31095 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31110--31110 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s parse = TRUE))[] [1702]) (./stats4-pkg.tex Chapter 11. [1703] [1704] [1705] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1706] [1707] [1708]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1709] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1710] [1711]) (./tcltk-pkg.tex [1712] Chapter 12. [1713] [1714] [1715] [1716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1717] [1718] [1719] Underfull \vbox (badness 10000) has occurred while \output is active [1720] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1732]) (./tools-pkg.tex Chapter 13. [1733] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1734] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1735] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1736] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1737] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1738] [1739] [1740] Underfull \hbox (badness 10000) in paragraph at lines 543--544 [][][]$\T1/pcr/m/n/10 https : / / partners . adobe . com / public / developer / en / opentype / [1741] [1742] [1743] [1744] [1745] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 905--905 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1747] Overfull \hbox (31.3804pt too wide) in paragraph at lines 953--953 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1748] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1749] [1750] Underfull \hbox (badness 5431) in paragraph at lines 1128--1131 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1751] Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1204--1207 []\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he r-it-ing from class [1752] [1753] Underfull \hbox (badness 10000) in paragraph at lines 1344--1347 []\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1754] [1755] [1756] [1757] [1758] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1667--1667 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1670--1670 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1677--1682 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1759] [1760] [1761]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1762] [1763] [1764] [1765] Underfull \hbox (badness 2644) in paragraph at lines 2149--2155 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgMacros \T1/ptm/m/n/10 func-tion firs t looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-age Overfull \hbox (101.58032pt too wide) in paragraph at lines 2183--2183 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1766] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2184--2184 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2211--2218 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2211--2218 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2211--2218 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1767] Underfull \hbox (badness 1342) in paragraph at lines 2263--2269 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1768] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2339--2339 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2352--2358 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1769] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2385--2385 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2394--2394 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2411--2411 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1770] [1771] [1772] [1773] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2676--2676 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1774] Underfull \hbox (badness 2486) in paragraph at lines 2721--2729 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1775] [1776] [1777] [1778] [1779] Underfull \hbox (badness 1072) in paragraph at lines 3099--3101 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1780] [1781] [1782] [1783] [1784] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3435--3435 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1785] [1786] [1787] [1788] Underfull \hbox (badness 4108) in paragraph at lines 3679--3686 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1789] [1790] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3779--3779 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3782--3782 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3816--3822 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1791] [1792] Underfull \hbox (badness 7832) in paragraph at lines 3938--3941 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1793] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4013--4013 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1794] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1795] [1796] [1797] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4210--4210 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4221--4224 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4237--4242 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4245--4251 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4245--4251 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1798] Underfull \hbox (badness 3758) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList \T1/ptm/m/n/10 ob- Underfull \hbox (badness 2865) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie d (for in-stance if there was [1799] [1800] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4457--4457 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4458--4458 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4470--4473 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', [1801] Underfull \hbox (badness 1742) in paragraph at lines 4474--4484 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4509--4515 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4509--4515 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 4537--4541 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1802] [1803] [1804]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1805] [1806] [1807] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1808] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1809] [1810] Underfull \hbox (badness 1946) in paragraph at lines 453--457 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1811] Overfull \hbox (0.78088pt too wide) in paragraph at lines 503--503 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 510--510 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 512--512 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] [1812] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 546--552 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1813] Underfull \hbox (badness 4505) in paragraph at lines 660--666 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1814] [1815] Underfull \hbox (badness 1603) in paragraph at lines 777--783 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 777--783 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1816] Overfull \hbox (6.78088pt too wide) in paragraph at lines 834--834 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1817] Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1818] Underfull \hbox (badness 10000) in paragraph at lines 1004--1007 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1819] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1087--1087 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1820] [1821] [1822] [1823] [1824] [1825] Underfull \hbox (badness 1859) in paragraph at lines 1458--1467 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1826] [1827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1559--1559 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1594--1594 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1828] [1829] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1740--1740 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1760--1760 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1830] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1816--1816 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1831] Underfull \hbox (badness 2213) in paragraph at lines 1857--1860 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1832] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via [1833] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1992--1992 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2015--2015 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1834] [1835] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2135--2135 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1836] Underfull \hbox (badness 1082) in paragraph at lines 2209--2213 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; Underfull \hbox (badness 10000) in paragraph at lines 2246--2248 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1837] Underfull \hbox (badness 1057) in paragraph at lines 2278--2285 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1838] [1839] [1840] Underfull \hbox (badness 10000) in paragraph at lines 2467--2469 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1841] [1842] [1843] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2703--2707 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1844] Underfull \hbox (badness 10000) in paragraph at lines 2757--2760 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set [1845] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2829--2829 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1846] Underfull \hbox (badness 2452) in paragraph at lines 2905--2908 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1847] [1848] [1849] [1850] [1851] [1852] [1853] Underfull \hbox (badness 1072) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1854] Underfull \hbox (badness 10000) in paragraph at lines 3441--3446 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3441--3446 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3441--3446 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1855] Underfull \hbox (badness 4660) in paragraph at lines 3563--3566 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to [1856] [1857] [1858] Underfull \hbox (badness 1565) in paragraph at lines 3772--3776 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of Underfull \hbox (badness 10000) in paragraph at lines 3793--3799 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1859] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3855--3855 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1860] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3883--3890 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1861] [1862] [1863] [1864] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4203--4203 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1865] [1866]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4274 ...mat Unordered and Ordered Lists}{format} [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1881] Underfull \hbox (badness 10000) in paragraph at lines 5311--5313 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1882] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1883] [1884] [1885] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1886] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 5612--5615 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1887] [1888] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1889] Underfull \hbox (badness 5091) in paragraph at lines 5870--5872 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL [1890] Overfull \hbox (44.55087pt too wide) in paragraph at lines 5886--5891 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 5899--5906 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1891] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., Underfull \hbox (badness 10000) in paragraph at lines 6016--6020 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , [1892] Underfull \hbox (badness 2376) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1314) in paragraph at lines 6089--6096 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1893] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6133--6133 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 6169--6173 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 6181--6184 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [1894] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6227--6227 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1895] [1896] Underfull \hbox (badness 4132) in paragraph at lines 6346--6348 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1897] [1898] [1899] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6504--6504 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1900] [1901] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6647--6647 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1902] Underfull \hbox (badness 10000) in paragraph at lines 6687--6689 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1903] [1904] Underfull \hbox (badness 10000) in paragraph at lines 6828--6830 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 6833--6835 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1905] [1906] [1907] Underfull \hbox (badness 1859) in paragraph at lines 7056--7059 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1908] Underfull \hbox (badness 1655) in paragraph at lines 7138--7141 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 7149--7149 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] [1909] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7153--7153 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 7161--7161 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1910] Underfull \hbox (badness 10000) in paragraph at lines 7246--7250 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1911] [1912] [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1915] [1916] [1917] Underfull \hbox (badness 10000) in paragraph at lines 7683--7688 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7683--7688 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 10000) in paragraph at lines 7690--7693 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7690--7693 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1918] [1919] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7806--7806 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7807--7807 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1920] [1921] [1922] [1923] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1924] Underfull \hbox (badness 10000) in paragraph at lines 8145--8149 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8145--8149 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1925] Underfull \hbox (badness 10000) in paragraph at lines 8258--8262 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8258--8262 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1926] [1927] Underfull \hbox (badness 10000) in paragraph at lines 8321--8325 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8321--8325 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1928] [1929] [1930] [1931] Underfull \hbox (badness 5203) in paragraph at lines 8652--8655 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1932] [1933] [1934] Underfull \hbox (badness 1776) in paragraph at lines 8878--8885 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set Overfull \hbox (30.78088pt too wide) in paragraph at lines 8902--8902 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1935] [1936] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9063--9063 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1937] [1938] [1939] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9244--9244 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [1940] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9330--9330 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] [1941] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9333--9333 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9338--9338 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1942] Underfull \hbox (badness 1077) in paragraph at lines 9410--9413 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [1943] [1944] [1945] [1946] [1947] [1948] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9850--9850 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1949] Underfull \hbox (badness 10000) in paragraph at lines 9937--9939 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1950] [1951] Underfull \hbox (badness 2181) in paragraph at lines 10060--10064 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10072--10076 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1952] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10090--10090 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10094--10094 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1953] [1954] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10226--10226 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1955] [1956] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10366--10366 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [1957] Underfull \hbox (badness 8075) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via Underfull \hbox (badness 6725) in paragraph at lines 10479--10488 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10479--10488 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10479--10488 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10479--10488 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1958] [1959] Underfull \hbox (badness 3646) in paragraph at lines 10605--10607 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [1960] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10643--10643 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1961] [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 10824--10828 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10855--10861 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1964] Underfull \hbox (badness 2012) in paragraph at lines 10950--10956 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use Underfull \hbox (badness 2096) in paragraph at lines 10963--10965 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 10966--10968 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10973--10976 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 10977--10980 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if [1965] Overfull \hbox (6.78088pt too wide) in paragraph at lines 11031--11031 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 11049--11060 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1966] [1967] Underfull \hbox (badness 2846) in paragraph at lines 11136--11146 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1968] [1969] Underfull \hbox (badness 10000) in paragraph at lines 11275--11278 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un- Underfull \hbox (badness 10000) in paragraph at lines 11275--11278 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11292--11295 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1970] [1971] Underfull \hbox (badness 2158) in paragraph at lines 11374--11377 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [1972] [1973] Underfull \hbox (badness 3333) in paragraph at lines 11557--11559 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [1974] [1975] [1976] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11722--11722 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 5970) in paragraph at lines 11755--11758 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11755--11758 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11766--11775 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1977] Overfull \hbox (36.7804pt too wide) in paragraph at lines 11810--11810 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [1978] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11841--11841 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 11848--11848 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11850--11850 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 12018--12020 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [1981] [1982] [1983] Underfull \hbox (badness 4492) in paragraph at lines 12175--12182 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12175--12182 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12175--12182 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [1984] [1985] Underfull \hbox (badness 2020) in paragraph at lines 12335--12351 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12335--12351 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [1986] Underfull \hbox (badness 5022) in paragraph at lines 12434--12438 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12441--12444 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 12441--12444 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] Underfull \hbox (badness 4467) in paragraph at lines 12950--12952 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 12963--12967 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to [1995] Overfull \hbox (36.87935pt too wide) in paragraph at lines 12977--12981 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 3557) in paragraph at lines 12983--12985 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12986--12988 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13037--13042 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with [1996] Underfull \hbox (badness 10000) in paragraph at lines 13045--13048 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13099--13099 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [1997] [1998] [1999] Underfull \hbox (badness 10000) in paragraph at lines 13287--13290 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; [2000] Overfull \hbox (42.18039pt too wide) in paragraph at lines 13303--13303 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13337--13337 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2001] Underfull \hbox (badness 1454) in paragraph at lines 13364--13368 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13389--13392 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and [2002] Underfull \hbox (badness 10000) in paragraph at lines 13434--13436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion Underfull \hbox (badness 3271) in paragraph at lines 13446--13450 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2003] [2004] [2005]) [2006] [2007] [2008] (./KernSmooth-pkg.tex Chapter 15. [2009] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2010] [2011] [2012] [2013] [2014] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2015] [2016] [2017] [2018]) (./MASS-pkg.tex Chapter 16. [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 7256) in paragraph at lines 1603--1605 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2415--2415 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2053] [2054] [2055] [2056] Underfull \hbox (badness 6559) in paragraph at lines 2693--2696 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2057] [2058] [2059] Underfull \hbox (badness 7362) in paragraph at lines 2863--2868 \T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 , Underfull \hbox (badness 3557) in paragraph at lines 2899--2907 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2899--2907 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2060] [2061] Underfull \hbox (badness 4686) in paragraph at lines 3031--3033 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 3045--3049 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2062] [2063] [2064] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3226--3226 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3233--3235 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2065] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1845) in paragraph at lines 4162--4164 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2078] [2079] [2080] [2081] [2082] [2083] [2084] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2085] [2086] Underfull \hbox (badness 10000) in paragraph at lines 4810--4813 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2087] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4888--4891 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2088] [2089] [2090] [2091] [2092] Underfull \hbox (badness 5681) in paragraph at lines 5288--5290 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5292--5295 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2093] Underfull \hbox (badness 1975) in paragraph at lines 5341--5343 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5927--5927 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2102] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5988--5988 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2103] [2104]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6130 ...sical N, P, K Factorial Experiment}{npk} [2105] Underfull \hbox (badness 1783) in paragraph at lines 6248--6252 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2106] [2107] [2108] [2109] Underfull \vbox (badness 10000) has occurred while \output is active [2110] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6546--6546 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2111] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2112] [2113] [2114] [2115] [2116] [2117] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7073--7073 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7090--7090 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7097--7104 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2118] Underfull \hbox (badness 10000) in paragraph at lines 7113--7115 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7168--7174 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2119] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7238--7238 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2120] [2121] Underfull \hbox (badness 5091) in paragraph at lines 7347--7350 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2122] [2123] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7477--7477 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2124] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7542--7542 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2125] [2126] [2127] [2128] [2129] [2130] Underfull \hbox (badness 4686) in paragraph at lines 7980--7982 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 7996--8000 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2131] [2132] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8099--8099 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8123--8127 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n /10 NA\T1/ptm/m/n/10 s are found. The [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9502--9502 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2153] Underfull \hbox (badness 1158) in paragraph at lines 9629--9632 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly), [2154] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9711--9711 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9713--9713 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9716--9716 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167]) (./Matrix-pkg.tex [2168] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2169] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2170] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2171] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2172] [2173] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2174] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2175] [2176] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2177] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2178] [2179] [2180] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2181] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2182]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2183pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] [2184] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2185] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2186] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2187] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2188] Underfull \hbox (badness 6445) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3861) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and [2189]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2190] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2191] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2192] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2193] [2194] [2195] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2196] [2197] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2198] Underfull \hbox (badness 4713) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2199] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2200] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2201] Underfull \hbox (badness 2707) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2202] Overfull \hbox (120.78088pt too wide) in paragraph at lines 2663--2663 []\T1/pcr/m/n/10 .symDiagonal(n, x = rep.int(1,n), uplo = "U", kind = if(is. logical(x)) "l" else "d")[] Overfull \hbox (120.78088pt too wide) in paragraph at lines 2664--2664 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind = if(is. logical(x)) "l" else "d")[] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2203] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2204] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 3803) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a [2205] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2206] [2207] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2208] Underfull \hbox (badness 1168) in paragraph at lines 3358--3361 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2209] [2210] Underfull \hbox (badness 4967) in paragraph at lines 3523--3527 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix", ...) \T1/ptm/m/n/10 or Overfull \hbox (2.39853pt too wide) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . [2211] Underfull \hbox (badness 6364) in paragraph at lines 3570--3573 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2212] [2213] Underfull \hbox (badness 10000) in paragraph at lines 3720--3725 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3720--3725 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 10000) in paragraph at lines 3730--3732 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3732--3735 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2214] Underfull \hbox (badness 10000) in paragraph at lines 3840--3843 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3840--3843 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the Underfull \hbox (badness 10000) in paragraph at lines 3843--3846 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3843--3846 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion [2215] Underfull \hbox (badness 6364) in paragraph at lines 3847--3850 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2216] Underfull \hbox (badness 4060) in paragraph at lines 3967--3970 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2217] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4007--4007 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4075--4079 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class [2218] Underfull \hbox (badness 10000) in paragraph at lines 4084--4087 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 4084--4087 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4089--4093 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2219] [2220] [2221] [2222] Underfull \hbox (badness 10000) in paragraph at lines 4377--4382 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2223] [2224] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4511--4511 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4514--4514 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4528--4528 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2225] [2226] Underfull \hbox (badness 10000) in paragraph at lines 4683--4685 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2227] [2228] Underfull \hbox (badness 10000) in paragraph at lines 4830--4835 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2229] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4911--4911 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4913--4913 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4917--4917 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4924--4924 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2230] [2231] Underfull \hbox (badness 4120) in paragraph at lines 5063--5066 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use [2232] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5100--5100 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5105--5105 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5112--5112 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5115--5115 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2233] Underfull \hbox (badness 1817) in paragraph at lines 5204--5213 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 5637) in paragraph at lines 5246--5248 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2234] Underfull \hbox (badness 3138) in paragraph at lines 5272--5274 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2235] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5339--5339 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] Underfull \hbox (badness 1603) in paragraph at lines 5360--5362 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5368--5373 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2236] [2237] [2238] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5597--5597 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2239] Underfull \hbox (badness 10000) in paragraph at lines 5678--5681 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5689--5689 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2240] Underfull \hbox (badness 1622) in paragraph at lines 5726--5731 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5726--5731 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2241] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5787--5787 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5788--5788 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5795--5795 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2242] [2243] Underfull \hbox (badness 1062) in paragraph at lines 5924--5927 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 2809) in paragraph at lines 5953--5956 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2244] Underfull \hbox (badness 2635) in paragraph at lines 6065--6070 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6065--6070 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class [2245] Underfull \hbox (badness 10000) in paragraph at lines 6073--6076 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6183--6193 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6183--6193 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2246] Underfull \hbox (badness 1184) in paragraph at lines 6265--6268 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2247] Underfull \hbox (badness 10000) in paragraph at lines 6363--6366 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2248] Underfull \hbox (badness 10000) in paragraph at lines 6438--6441 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2249] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6454--6454 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Underfull \hbox (badness 2443) in paragraph at lines 6493--6499 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6493--6499 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6514--6517 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2250] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6584--6584 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2251] [2252] Underfull \hbox (badness 6268) in paragraph at lines 6720--6723 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2253] Underfull \hbox (badness 5036) in paragraph at lines 6744--6748 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6744--6748 \T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e mpty'' [][]sparse-Ma-trix[][][], as does [2254]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6837 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6917--6920 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6922--6925 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6922--6925 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6940--6943 Underfull \hbox (badness 7326) in paragraph at lines 6950--6952 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re -lies on a cor-rect [2255]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7013 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7121 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7221 ...tcrossprod}{matrix-products}{tcrossprod} [2256] Underfull \hbox (badness 1881) in paragraph at lines 7319--7325 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2257pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7381 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7381 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7392--7395 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 7392--7395 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7395--7400 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7404--7406 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7406--7408 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7410--7411 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2258] [2259] Underfull \hbox (badness 1062) in paragraph at lines 7591--7594 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2260] Underfull \hbox (badness 2809) in paragraph at lines 7625--7628 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2261] Underfull \hbox (badness 10000) in paragraph at lines 7677--7679 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter [2262] Underfull \hbox (badness 1406) in paragraph at lines 7717--7721 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7717--7721 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2263] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7815--7815 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2264] Underfull \hbox (badness 2635) in paragraph at lines 7880--7885 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7880--7885 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7888--7891 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2265] [2266] Underfull \hbox (badness 10000) in paragraph at lines 8082--8084 []\T1/ptm/m/n/10 fast [2267]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8122 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8122 \HeaderA{norm}{Matrix Norms}{norm} [2268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8209--8209 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8210--8210 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8211--8211 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8324--8334 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2269] Underfull \hbox (badness 1184) in paragraph at lines 8395--8398 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2270] Underfull \hbox (badness 10000) in paragraph at lines 8485--8488 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2271] Underfull \hbox (badness 10000) in paragraph at lines 8561--8564 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2272] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8577--8577 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2273] Underfull \hbox (badness 10000) in paragraph at lines 8687--8689 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8703--8705 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8709--8713 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2274] [2275] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8788--8788 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8793--8793 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8798--8798 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8821--8831 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8821--8831 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2276] [2277]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8922 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8968--8971 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 8995--8995 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] [2278] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9006--9006 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9024--9024 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9032--9032 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=1e-15))## just = X, incl. co rrect colnames[] [2279] Underfull \hbox (badness 10000) in paragraph at lines 9085--9091 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9102--9105 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2280] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9174--9174 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9195--9195 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9196--9196 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2281]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco nd}) has been already used, duplicate ignored \relax l.9215 ... the Reciprocal Condition Number}{rcond} [2282] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9328--9328 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2283] [2284] [2285] Underfull \hbox (badness 10000) in paragraph at lines 9511--9513 []\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably Underfull \hbox (badness 1325) in paragraph at lines 9517--9525 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2286] [2287] Underfull \hbox (badness 1558) in paragraph at lines 9662--9665 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2288] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9724--9724 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9728--9728 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2289]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9790 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9887--9887 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9892--9892 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2290] Underfull \hbox (badness 6047) in paragraph at lines 9927--9939 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9944--9947 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9949--9950 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9953--9960 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9953--9960 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 9966--9976 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 9966--9976 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2291] Underfull \hbox (badness 1194) in paragraph at lines 10000--10002 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10014--10017 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10023--10024 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10029--10031 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10033--10034 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10041--10044 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10059--10059 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10063--10063 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2292] Underfull \hbox (badness 10000) in paragraph at lines 10084--10087 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10112--10114 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10120--10123 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the [2293] Underfull \hbox (badness 10000) in paragraph at lines 10131--10135 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10131--10135 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10142--10144 []\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in -di-cat-ing if the re-sult must be a [2294] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10219--10219 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10220--10220 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10221--10221 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2295] [2296] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10405--10405 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10406--10406 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2297] Underfull \hbox (badness 4621) in paragraph at lines 10446--10450 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2298] Underfull \hbox (badness 10000) in paragraph at lines 10522--10525 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10534--10534 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10538--10538 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10539--10539 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10544--10544 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10547--10547 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2299] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10570--10570 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10571--10571 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10597--10597 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10599--10599 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10601--10601 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2300] Underfull \hbox (badness 10000) in paragraph at lines 10694--10702 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10715--10719 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2301] Underfull \hbox (badness 10000) in paragraph at lines 10745--10749 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10785 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2302] [2303] Underfull \hbox (badness 1430) in paragraph at lines 10915--10917 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10943--10943 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 10971--10973 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2304] Underfull \hbox (badness 2970) in paragraph at lines 11104--11110 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11104--11110 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2305] Underfull \hbox (badness 10000) in paragraph at lines 11155--11158 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11177--11180 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2306] Underfull \hbox (badness 10000) in paragraph at lines 11195--11200 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11210--11212 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2307] [2308] Underfull \hbox (badness 3525) in paragraph at lines 11328--11332 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11335--11341 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2309] Underfull \hbox (badness 10000) in paragraph at lines 11430--11434 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11430--11434 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11446--11451 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 1259) in paragraph at lines 11446--11451 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11454--11459 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2310] Underfull \hbox (badness 2057) in paragraph at lines 11526--11528 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2311] [2312] Underfull \hbox (badness 6641) in paragraph at lines 11612--11615 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11652--11656 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11652--11656 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2313] Underfull \hbox (badness 7649) in paragraph at lines 11759--11761 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2314] [2315] [2316] Underfull \hbox (badness 7362) in paragraph at lines 11960--11962 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2317] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11998--11998 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11999--11999 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2318] [2319] Underfull \hbox (badness 6910) in paragraph at lines 12249--12251 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2320] [2321] [2322]) (./boot-pkg.tex Chapter 18. [2323] [2324] [2325] [2326] [2327] [2328] [2329] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2330] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2331] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2332] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2333] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2334] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2335] [2336] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues [2337] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2338] [2339] [2340] [2341] [2342] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2343] [2344] [2345] [2346] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2347] [2348] [2349] [2350] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] Underfull \vbox (badness 10000) has occurred while \output is active [2351] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2352] [2353] [2354] [2355] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. [2356] Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2357] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2358] [2359] [2360] [2361] [2362] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2363] [2364] [2365] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2366] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2367] [2368] [2369] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2370] [2371] [2372] [2373] [2374] [2375] [2376] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2377] [2378] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2379] [2380] [2381] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2383] [2384] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2385] [2386] [2387] [2388] [2389] [2390] [2391] [2392] [2393] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2394] [2395] [2396] [2397] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2399] [2400] [2401] [2402] [2403] [2404] [2405] [2406] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2407] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2408] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2409] [2410] [2411] [2412] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2413] [2414] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2415] [2416] [2417] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2418] [2419] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427]) (./class-pkg.tex [2428] Chapter 19. [2429] [2430] [2431] [2432] [2433] [2434] [2435] [2436] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2437] [2438] [2439] [2440] [2441] [2442] [2443] [2444]) (./cluster-pkg.tex Chapter 20. [2445] Underfull \hbox (badness 3098) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2446] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2447] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2448] [2449] Underfull \vbox (badness 10000) has occurred while \output is active [2450] [2451] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2452] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2453] Overfull \hbox (66.78088pt too wide) in paragraph at lines 636--636 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2454] Underfull \hbox (badness 3078) in paragraph at lines 682--685 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2455] Underfull \hbox (badness 2941) in paragraph at lines 771--774 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2456] Overfull \hbox (9.78043pt too wide) in paragraph at lines 809--809 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2457] Underfull \hbox (badness 10000) in paragraph at lines 857--859 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2458] Overfull \hbox (24.78088pt too wide) in paragraph at lines 922--922 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2459] Underfull \hbox (badness 4872) in paragraph at lines 968--970 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 982--986 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2460] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1089--1089 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2461] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1144--1144 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2462] Underfull \hbox (badness 4144) in paragraph at lines 1176--1180 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2463] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1252--1252 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1258--1258 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2464] [2465] Underfull \hbox (badness 10000) in paragraph at lines 1397--1402 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*, cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1445--1448 Underfull \hbox (badness 10000) in paragraph at lines 1462--1466 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , [2466] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1486--1486 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1496--1496 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2467] Underfull \hbox (badness 5741) in paragraph at lines 1536--1539 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1602--1602 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2469] Underfull \hbox (badness 5008) in paragraph at lines 1719--1727 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where [2470] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1810--1810 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] [2471] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1829--1829 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2472] [2473] [2474] [2475] Underfull \hbox (badness 10000) in paragraph at lines 2137--2139 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2148--2151 Underfull \hbox (badness 3179) in paragraph at lines 2162--2168 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2476] [2477] [2478] Underfull \hbox (badness 10000) in paragraph at lines 2320--2323 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2479] Underfull \hbox (badness 1292) in paragraph at lines 2388--2391 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2397--2399 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2420--2423 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2480] [2481] [2482] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2634--2634 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2483] [2484] [2485] Underfull \hbox (badness 1067) in paragraph at lines 2820--2825 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2486] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2487] [2488] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2982--2982 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2489] [2490] [2491] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3178--3178 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2492] Underfull \hbox (badness 10000) in paragraph at lines 3246--3249 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2493] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3296--3296 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3297--3297 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2494] [2495] [2496] Underfull \hbox (badness 10000) in paragraph at lines 3482--3485 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for Underfull \hbox (badness 3471) in paragraph at lines 3482--3485 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2497] Underfull \hbox (badness 10000) in paragraph at lines 3545--3550 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2498] Underfull \hbox (badness 4621) in paragraph at lines 3607--3612 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3607--3612 \T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1 /ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider Underfull \hbox (badness 6268) in paragraph at lines 3619--3622 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2499] [2500] [2501] Underfull \hbox (badness 10000) in paragraph at lines 3804--3807 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3835--3838 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2502] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3888--3888 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3899--3901 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2503] [2504] [2505] [2506] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4092--4092 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4094--4094 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4123--4128 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2507] Underfull \hbox (badness 10000) in paragraph at lines 4190--4198 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2508] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4232--4232 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4241--4241 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4243--4243 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4246--4246 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4248--4248 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4262--4262 [] \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t olerance = 0))[] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2517] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2518] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2519] [2520] [2521]) (./foreign-pkg.tex [2522] Chapter 22. [2523] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2524] [2525] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2526] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2527] [2528] [2529] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2530] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli cated_"\T1/ptm/m/n/10 ) if [2531] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2532] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2534] [2535] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2536] [2537] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2538] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2539] [2540] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2541] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2542] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2543] Underfull \hbox (badness 6725) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by [2544]) (./lattice-pkg.tex Chapter 23. [2545] [2546] [2547] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2548] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2549] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2550] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2551] [2552] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2553] [2554] [2555] [2556] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2557] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2558] [2559] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2560] [2561] [2562] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2563] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2564] Underfull \vbox (badness 10000) has occurred while \output is active [2565] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2566] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2567] Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2568] [2569] [2570] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2571] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2572] [2573] [2574] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2575] [2576] [2577] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2578] [2579] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2580] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2581] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast er[][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2883--2885 []\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T 1/ptm/m/n/10 when [2582] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2583] [2584] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2585] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2586] [2587] [2588] [2589]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2590] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2591] [2592] [2593] [2594] [2595] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2596] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2597] [2598] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4105--4109 \T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se t-tings (ob-tained by [2599] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2600] [2601] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl ot.polygon \T1/ptm/m/n/10 and [2602] [2603] [2604] [2605] [2606] [2607] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2608] [2609] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2610] [2611] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2612] [2613] [2614] [2615] [2616] [2617] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2618] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef t of pan-els us-ing Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2619] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh ich is to draw a strip ap-pro-pri-ate for [2620] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2621] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2622] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2623] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are used (in com-bi-na-tion with [2624] [2625] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2626] [2627] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2628] [2629] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2630] [2631] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2632] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2633] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2634] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2635] [2636] [2637] [2638] [2639] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2640] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2641] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu nc-tion is passed [2642] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2643] [2644] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2645] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2646] [2647] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2648] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2649] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2650] [2651] [2652] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2653] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2662] [2663] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2664] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2665] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2666] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2667] [2668] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2669] [2670] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2671] Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left, right, left.name, right.name, condition Overfull \hbox (104.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name , right.x.name, right.y.name, condition [2672] [2673] [2674] [2675] [2676] [2677] [2678] Underfull \hbox (badness 4205) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2679] [2680] [2681]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2682] [2683] [2684] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes \T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2685] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2686]) (./mgcv-pkg.tex Chapter 24. [2687] [2688] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2689] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2690] [2691] [2692] Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 359--366 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2693] [2694] [2695] [2696] Underfull \hbox (badness 2922) in paragraph at lines 595--596 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2697] [2698] Underfull \hbox (badness 1158) in paragraph at lines 666--668 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2699] Underfull \hbox (badness 1259) in paragraph at lines 729--730 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2700] Underfull \vbox (badness 10000) has occurred while \output is active [2701] [2702] [2703] [2704] [2705] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1078--1078 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1084--1084 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] [2706] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1091--1091 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1093--1093 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",ylim=c(0,1),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2707] [2708] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1231--1231 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2709] [2710] [2711] [2712] [2713] [2714] [2715] [2716] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1686--1686 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2717] [2718] Underfull \vbox (badness 4913) has occurred while \output is active [2719] [2720] [2721] [2722] Underfull \hbox (badness 1052) in paragraph at lines 2061--2069 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2078--2078 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2090--2093 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also [2723] Underfull \hbox (badness 1142) in paragraph at lines 2103--2107 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2129--2134 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2724] [2725] [2726] Underfull \hbox (badness 1043) in paragraph at lines 2294--2300 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2727] [2728] Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2426--2432 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2729] Underfull \vbox (badness 10000) has occurred while \output is active [2730] Underfull \vbox (badness 10000) has occurred while \output is active [2731] [2732] [2733] [2734] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2748--2748 [] \T1/pcr/m/n/10 keepData=FALSE,scale.est="fletcher",edge.correct= FALSE)[] [2735] [2736] [2737] [2738] [2739] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3075--3075 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3078--3078 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2740] [2741] [2742] [2743] [2744] [2745] Underfull \hbox (badness 5189) in paragraph at lines 3439--3443 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2746] Underfull \vbox (badness 10000) has occurred while \output is active [2747] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3556--3556 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2748] [2749] Underfull \hbox (badness 1184) in paragraph at lines 3725--3729 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2750] [2751] [2752] [2753] [2754] [2755] [2756] [2757] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4171--4171 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2758] [2759] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4321--4321 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2760] [2761] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4415--4415 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] Underfull \hbox (badness 1142) in paragraph at lines 4446--4450 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2762] Underfull \hbox (badness 10000) in paragraph at lines 4515--4524 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2763] [2764] Underfull \hbox (badness 5970) in paragraph at lines 4632--4638 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4632--4638 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2765] Underfull \vbox (badness 10000) has occurred while \output is active [2766] [2767] [2768] Underfull \hbox (badness 1577) in paragraph at lines 4912--4915 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 4919--4920 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2769] [2770] [2771] [2772] [2773] [2774] [2775] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5314--5314 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2776] [2777] [2778] [2779] [2780] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5638--5638 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2781] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5640--5640 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5661--5665 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2782] [2783] [2784] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5797--5797 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in i,n.chains=1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5828--5828 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in i,n.chains=1)[] Underfull \vbox (badness 10000) has occurred while \output is active [2785] [2786] Overfull \hbox (72.78088pt too wide) in paragraph at lines 5902--5902 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2787] [2788] [2789] Underfull \vbox (badness 10000) has occurred while \output is active [2790] [2791] [2792] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6281--6281 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [2793] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6308--6308 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2794] [2795] [2796] [2797] [2798] [2799] Underfull \vbox (badness 4366) has occurred while \output is active [2800] [2801] Underfull \hbox (badness 1242) in paragraph at lines 6851--6852 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2802] [2803] [2804] [2805] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7001--7001 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7020--7020 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2806] [2807] [2808] [2809] [2810] [2811] [2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] Underfull \vbox (badness 10000) has occurred while \output is active [2824] [2825] Underfull \hbox (badness 10000) in paragraph at lines 8240--8243 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8240--8243 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8240--8243 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2826] Underfull \hbox (badness 10000) in paragraph at lines 8296--8299 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8296--8299 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2827] [2828] [2829] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8516--8516 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8517--8517 [] \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla b=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8520--8520 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2830] [2831] [2832] Underfull \hbox (badness 1629) in paragraph at lines 8675--8680 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2833] [2834] [2835] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8876--8876 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2836] [2837] [2838] [2839] [2840] [2841] Underfull \vbox (badness 10000) has occurred while \output is active [2842] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9304--9304 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2843] Underfull \hbox (badness 1205) in paragraph at lines 9342--9344 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9342--9344 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9348--9353 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2844] Underfull \hbox (badness 1205) in paragraph at lines 9432--9434 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9432--9434 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2845] Underfull \hbox (badness 10000) in paragraph at lines 9501--9504 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9501--9504 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2846] [2847] [2848] Underfull \hbox (badness 1253) in paragraph at lines 9631--9633 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2849] [2850] Underfull \vbox (badness 10000) has occurred while \output is active [2851] Underfull \hbox (badness 1946) in paragraph at lines 9809--9816 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 9809--9816 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 9809--9816 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 9817--9820 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 9817--9820 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2852] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9883--9883 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] [2853] Underfull \hbox (badness 10000) in paragraph at lines 9912--9915 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2854] [2855] [2856] [2857] [2858] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10199--10199 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2859] [2860] [2861] [2862] [2863] Underfull \vbox (badness 10000) has occurred while \output is active [2864] Underfull \hbox (badness 3861) in paragraph at lines 10540--10543 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10547--10547 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10560--10564 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2865] Underfull \hbox (badness 10000) in paragraph at lines 10600--10604 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2866] [2867] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10741--10741 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 10752--10757 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2868] [2869] Underfull \hbox (badness 1803) in paragraph at lines 10829--10833 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 10841--10853 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 10858--10862 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 10858--10862 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2870] [2871] [2872] Underfull \hbox (badness 6876) in paragraph at lines 11053--11059 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like [2873] Underfull \hbox (badness 10000) in paragraph at lines 11094--11095 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2874] [2875] Underfull \hbox (badness 10000) in paragraph at lines 11212--11213 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2876] [2877] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11277--11277 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11288--11288 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11289--11289 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11294--11294 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11300--11300 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11301--11301 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] Underfull \vbox (badness 10000) has occurred while \output is active [2878] Underfull \hbox (badness 10000) in paragraph at lines 11370--11372 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11370--11372 \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs", ...) \T1/ptm/m/n/10 or [2879] [2880] Underfull \hbox (badness 10000) in paragraph at lines 11498--11499 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2881] [2882] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11579--11579 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11580--11580 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2883] Underfull \hbox (badness 7613) in paragraph at lines 11618--11621 \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p tm/m/n/10 pro-duced by the [2884] [2885] Underfull \hbox (badness 10000) in paragraph at lines 11727--11728 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2886] [2887] [2888] [2889] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11964--11964 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] Underfull \hbox (badness 10000) in paragraph at lines 12009--12011 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2890] [2891] Underfull \vbox (badness 10000) has occurred while \output is active [2892] Underfull \hbox (badness 10000) in paragraph at lines 12168--12171 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12168--12171 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12168--12171 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2893] [2894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12250--12250 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12295--12301 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12295--12301 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2895] [2896] [2897] Underfull \vbox (badness 10000) has occurred while \output is active [2898] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12509--12509 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2899] [2900] Underfull \hbox (badness 10000) in paragraph at lines 12612--12620 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 12638--12639 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2901] [2902] [2903] [2904] Underfull \hbox (badness 3396) in paragraph at lines 12899--12902 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2905] Underfull \hbox (badness 10000) in paragraph at lines 12944--12946 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2906] [2907] [2908] [2909] Underfull \hbox (badness 10000) in paragraph at lines 13168--13171 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13168--13171 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [2910] Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13201--13205 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [2911] [2912] [2913] [2914] Underfull \hbox (badness 2158) in paragraph at lines 13442--13442 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2915] Overfull \hbox (48.78088pt too wide) in paragraph at lines 13517--13517 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2916] [2917] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13651--13651 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2918] [2919] Underfull \hbox (badness 4846) in paragraph at lines 13779--13782 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [2920] [2921] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] [2931] [2932] [2933] Underfull \hbox (badness 10000) in paragraph at lines 14604--14612 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 14604--14612 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2934] [2935] [2936] [2937] Overfull \hbox (24.78088pt too wide) in paragraph at lines 14876--14876 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2938] [2939] [2940] [2941] [2942] [2943] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15170--15170 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15171--15171 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15183--15183 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2944] [2945] [2946]) (./nlme-pkg.tex Chapter 25. [2947] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2948] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2949] [2950] [2951] [2952] [2953] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2954] [2955] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [2964] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [2965] [2966] [2967] [2968] [2969] [2970] [2971] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [2972] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [2973] [2974] [2975] [2976] [2977] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [2978] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [2979] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [2980] [2981] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [2982] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2983] [2984] [2985] [2986] [2987] [2988] [2989] [2990] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001] [3002] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3003] [3004] [3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3027] [3028] [3029] [3030] [3031] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3032] [3033] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041] [3042] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3043] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3044] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3045] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3046] [3047] [3048] [3049] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3050] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , [3051] Underfull \hbox (badness 10000) in paragraph at lines 6717--6719 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3052] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6747--6747 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3053] [3054] [3055] Underfull \hbox (badness 10000) in paragraph at lines 6990--6997 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3056] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7007--7007 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7015--7015 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7037--7039 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3057] [3058] [3059] Underfull \hbox (badness 10000) in paragraph at lines 7252--7257 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3060] [3061] [3062] Underfull \hbox (badness 10000) in paragraph at lines 7404--7412 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7404--7412 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 1817) in paragraph at lines 7404--7412 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7427--7430 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3063] [3064] [3065] Underfull \hbox (badness 3354) in paragraph at lines 7642--7644 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3066] [3067] [3068] [3069] [3070] [3071] Underfull \hbox (badness 1642) in paragraph at lines 8034--8056 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3072] [3073] Underfull \hbox (badness 10000) in paragraph at lines 8154--8171 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8154--8171 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8197--8197 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8206--8228 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3074] [3075] [3076] [3077] [3078] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8471--8471 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8516--8518 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3079] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8554--8554 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8561 \aliasA{sigma}{lmeObject}{sigma} [3080] [3081] [3082] Underfull \hbox (badness 10000) in paragraph at lines 8722--8734 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] Underfull \hbox (badness 10000) in paragraph at lines 9313--9320 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9324--9324 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3092] Underfull \hbox (badness 6300) in paragraph at lines 9406--9409 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3093] [3094] [3095] [3096]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9675 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3097] Underfull \hbox (badness 10000) in paragraph at lines 9695--9698 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9739--9742 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9739--9742 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3098] [3099] [3100] Underfull \hbox (badness 2435) in paragraph at lines 9913--9918 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3101] [3102] [3103] [3104] [3105] Underfull \hbox (badness 7291) in paragraph at lines 10203--10205 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3106] [3107] [3108] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10419--10419 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3109] Underfull \hbox (badness 1596) in paragraph at lines 10448--10474 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3110] [3111] [3112] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10624--10624 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3113] [3114] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10775--10775 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] [3115] Underfull \hbox (badness 10000) in paragraph at lines 10821--10823 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Underfull \hbox (badness 1092) in paragraph at lines 10833--10836 []\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr /m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used Overfull \hbox (9.78043pt too wide) in paragraph at lines 10856--10856 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3116] [3117] [3118] [3119] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11112--11112 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] Underfull \hbox (badness 6268) in paragraph at lines 11891--11901 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3132] [3133] [3134] [3135] Underfull \hbox (badness 10000) in paragraph at lines 12152--12158 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3136] [3137] [3138] [3139] [3140] Underfull \hbox (badness 6876) in paragraph at lines 12474--12476 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3141] [3142] Underfull \hbox (badness 2452) in paragraph at lines 12630--12637 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3143] Underfull \hbox (badness 10000) in paragraph at lines 12695--12701 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13647--13647 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3158] Underfull \hbox (badness 10000) in paragraph at lines 13674--13677 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 6016) in paragraph at lines 13702--13705 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13702--13705 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13709--13712 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13717--13724 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13717--13724 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner [3159] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13774--13774 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13781--13784 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13781--13784 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle [3160] Underfull \hbox (badness 4582) in paragraph at lines 13809--13812 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13809--13812 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13813--13816 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3161] Underfull \hbox (badness 10000) in paragraph at lines 13889--13892 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 1472) in paragraph at lines 13914--13921 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3162] Underfull \hbox (badness 10000) in paragraph at lines 13983--13985 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3163] [3164] [3165] [3166] Underfull \hbox (badness 1540) in paragraph at lines 14198--14203 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14245--14247 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3167] [3168] [3169] [3170] [3171] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14489--14489 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15142 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15142 ...Extract Random Effects}{random.effects} [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] Underfull \hbox (badness 1009) in paragraph at lines 15799--15808 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3191] [3192] [3193] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15946--15946 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3194] [3195] [3196] [3197] Underfull \hbox (badness 10000) in paragraph at lines 16224--16242 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16224--16242 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3198] Underfull \hbox (badness 10000) in paragraph at lines 16281--16287 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3199] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16312--16312 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3200] [3201] [3202] [3203] [3204] [3205] [3206] Underfull \hbox (badness 1728) in paragraph at lines 16801--16804 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3207] [3208] [3209] [3210] [3211] Underfull \hbox (badness 1867) in paragraph at lines 17136--17145 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17136--17145 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3212] Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17200--17208 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , [3213] [3214] [3215] [3216] Underfull \hbox (badness 10000) in paragraph at lines 17447--17454 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 10000) in paragraph at lines 17977--17987 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17977--17987 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18015--18020 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3225] Underfull \hbox (badness 3579) in paragraph at lines 18079--18084 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3226] Underfull \hbox (badness 3579) in paragraph at lines 18142--18147 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3227] Underfull \hbox (badness 1577) in paragraph at lines 18203--18205 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18205--18210 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3228] Underfull \hbox (badness 3579) in paragraph at lines 18268--18273 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3229] Underfull \hbox (badness 10000) in paragraph at lines 18301--18310 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18301--18310 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18340--18345 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3230] [3231] [3232] Underfull \hbox (badness 1009) in paragraph at lines 18489--18498 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3233] [3234] Underfull \hbox (badness 1009) in paragraph at lines 18623--18632 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3235] [3236] [3237] [3238] [3239] [3240] [3241] [3242]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3243] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3244] [3245] [3246] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3247] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3248] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3249] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3250]) (./rpart-pkg.tex Chapter 27. [3251] [3252] [3253] [3254] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3255] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3256] [3257] [3258] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3259] [3260] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3261] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3262] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3263] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3264] [3265] [3266] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3267] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3268] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3269] [3270] [3271] [3272] [3273] [3274] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3275] [3276] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3277] [3278] [3279]) (./spatial-pkg.tex [3280] Chapter 28. [3281] [3282] [3283] [3284] [3285] [3286] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3287] [3288] [3289] [3290] [3291] [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299]) (./survival-pkg.tex [3300] Chapter 29. [3301] [3302] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3303] [3304] Overfull \hbox (42.78088pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho d, rownames) Overfull \hbox (42.78088pt too wide) in paragraph at lines 279--279 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho d, rownames)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.319 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.319 ... Myelogenous Leukemia survival data}{aml} [3305] [3306] Overfull \hbox (9.78043pt too wide) in paragraph at lines 416--416 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 418--418 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3307] Overfull \hbox (6.78088pt too wide) in paragraph at lines 455--455 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3308] [3309] Underfull \vbox (badness 10000) has occurred while \output is active [3310] Overfull \hbox (36.78088pt too wide) in paragraph at lines 654--654 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 655--655 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3311] [3312] Overfull \hbox (9.78043pt too wide) in paragraph at lines 798--798 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3313] [3314] [3315] Underfull \hbox (badness 1097) in paragraph at lines 968--970 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 988--988 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3316] [3317] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1103--1103 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3318]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1171 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3319] [3320] [3321] [3322] [3323] [3324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1623--1623 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3325] [3326] [3327] [3328] [3329] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1988--1988 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3330] [3331] [3332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2237--2237 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3333] [3334] [3335] [3336] [3337] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2554--2554 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Underfull \hbox (badness 1389) in paragraph at lines 2567--2569 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3338] Underfull \hbox (badness 1048) in paragraph at lines 2621--2623 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3339] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2698--2698 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] [3340] [3341] [3342] [3343] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2945--2945 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3344] [3345] [3346] [3347] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3211--3211 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3348] [3349] [3350] [3351] Underfull \vbox (badness 10000) has occurred while \output is active [3352] [3353] [3354] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3620--3620 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc ale=1,[] [3355] [3356] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3809--3809 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3357] [3358] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3925--3925 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3359] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4015--4015 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3360] [3361] [3362] Underfull \hbox (badness 1852) in paragraph at lines 4163--4165 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3363] [3364] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4297--4297 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4298--4298 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3365] [3366] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4462--4462 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3367] Underfull \hbox (badness 1540) in paragraph at lines 4517--4520 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4564--4564 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3368] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4585--4585 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3369] [3370] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4732--4732 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] [3371] Underfull \vbox (badness 10000) has occurred while \output is active [3372] [3373] [3374] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5017--5017 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 []\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response" \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 \T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5029--5034 \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n /10 . See the La-TeX doc-u-men-ta-tion [3375] [3376] [3377] [3378] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5302--5302 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5303--5303 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] [3379] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5358--5358 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3380] [3381] [3382] [3383] [3384] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5693--5693 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5694--5694 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3385] [3386] [3387] [3388] Overfull \hbox (54.78088pt too wide) in paragraph at lines 5995--5995 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3389] [3390] [3391] [3392] Underfull \hbox (badness 10000) in paragraph at lines 6255--6264 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3393] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6365--6365 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] [3394] Underfull \hbox (badness 1038) in paragraph at lines 6407--6413 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival Underfull \hbox (badness 3000) in paragraph at lines 6429--6431 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, [3395] Overfull \hbox (48.78088pt too wide) in paragraph at lines 6459--6459 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3396] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6545--6545 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3397] [3398] [3399] Underfull \hbox (badness 10000) in paragraph at lines 6770--6775 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , Overfull \hbox (18.78088pt too wide) in paragraph at lines 6791--6791 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T RUE, id,[] [3400] [3401] [3402] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7007--7007 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3403] Underfull \hbox (badness 6332) in paragraph at lines 7114--7119 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3404] [3405] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7294--7294 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3406] [3407] [3408] [3409] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3410] Underfull \hbox (badness 1354) in paragraph at lines 7622--7626 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3411] [3412] Underfull \hbox (badness 2035) in paragraph at lines 7798--7805 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 7798--7805 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 7798--7805 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3413] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7874--7874 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3414] [3415] [3416] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8032--8032 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3417] [3418] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8164--8164 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8167--8167 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3419] [3420] [3421] [3422] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8464--8464 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8465--8465 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8471--8471 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8473--8473 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3423] [3424] [3425] [3426] Underfull \vbox (badness 10000) has occurred while \output is active [3427] [3428]) (./fullrefman.ind [3429] [3430] [3431] [3432] [3433] [3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2186--2188 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2188--2190 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2190--2192 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in 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cbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 5902--5904 []\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 5904--5906 []\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method [3482] Overfull \hbox (10.01662pt too wide) in paragraph at lines 6072--6074 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Underfull \vbox (badness 1484) has occurred while \output is active Underfull \vbox (badness 1117) has occurred while \output is active [3483] [3484] [3485] Overfull \hbox (50.8567pt too wide) in paragraph at lines 6443--6445 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 6445--6447 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 6447--6449 []\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method Overfull \hbox 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coerce,dgeMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6541--6543 []\T1/pcr/m/n/10 coerce,dgeMatrix,dsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6543--6545 []\T1/pcr/m/n/10 coerce,dgeMatrix,dtrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6545--6547 []\T1/pcr/m/n/10 coerce,dgeMatrix,lgeMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 6549--6551 []\T1/pcr/m/n/10 coerce,dgeMatrix,triangularMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 6551--6553 []\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6553--6555 []\T1/pcr/m/n/10 coerce,dgTMatrix,dgCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6555--6557 []\T1/pcr/m/n/10 coerce,dgTMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 6557--6559 []\T1/pcr/m/n/10 coerce,dgTMatrix,dsTMatrix-method 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too wide) in paragraph at lines 7097--7099 []\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7101--7103 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7103--7105 []\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7105--7107 []\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7107--7109 []\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7109--7111 []\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7113--7115 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7115--7117 []\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7117--7119 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coerce,ngTMatrix,lgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7137--7139 []\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7143--7145 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7145--7147 []\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7147--7149 []\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7149--7151 []\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method [3493] Overfull \hbox (50.8567pt too wide) in paragraph at lines 7151--7153 []\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7165--7167 []\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7167--7169 []\T1/pcr/m/n/10 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coerce,nsparseVector,isparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7189--7191 []\T1/pcr/m/n/10 coerce,nsparseVector,lsparseVector-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (56.8567pt too wide) in paragraph at lines 7191--7193 []\T1/pcr/m/n/10 coerce,nsparseVector,zsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7193--7195 []\T1/pcr/m/n/10 coerce,nspMatrix,dspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7195--7197 []\T1/pcr/m/n/10 coerce,nspMatrix,lspMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7197--7199 []\T1/pcr/m/n/10 coerce,nspMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7199--7201 []\T1/pcr/m/n/10 coerce,nspMatrix,nsyMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7201--7203 []\T1/pcr/m/n/10 coerce,nsTMatrix,dsTMatrix-method Overfull \hbox (8.8567pt too wide) in 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coerce,ntCMatrix,dsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7225--7227 []\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7229--7231 []\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method [3494] Overfull \hbox (8.8567pt too wide) in paragraph at lines 7231--7233 []\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7235--7237 []\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7237--7239 []\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7239--7241 []\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7241--7243 []\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7243--7245 []\T1/pcr/m/n/10 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lines 7389--7391 []\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7391--7393 []\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7393--7395 []\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7395--7397 []\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7397--7399 []\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7399--7401 []\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method [3496] Underfull \vbox (badness 1348) has occurred while \output is active Overfull \hbox (62.8567pt too wide) in paragraph at lines 7510--7512 []\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7516--7518 []\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 7528--7530 []\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7530--7532 []\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 7544--7546 []\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method [3497] [3498] [3499] Overfull \hbox (14.8567pt too wide) in paragraph at lines 7888--7890 []\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 7890--7892 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 7892--7894 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 7894--7896 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (32.8567pt too 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determinant,sparseMatrix,logical-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8396--8398 []\T1/pcr/m/n/10 determinant,sparseMatrix,missing-method [3504] [3505] Overfull \hbox (10.01662pt too wide) in paragraph at lines 8617--8619 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Underfull \vbox (badness 1226) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 8667--8669 []\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8669--8671 []\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method [3506] [3507] Overfull \hbox (46.01662pt too wide) in paragraph at lines 8874--8876 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3508] Overfull \hbox (8.8567pt too wide) in paragraph at lines 9082--9084 []\T1/pcr/m/n/10 expand,MatrixFactorization-method Overfull \hbox (10.01662pt too wide) in 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groupGenericFunctionWithTrace-class [3517] [3518] [3519] Underfull \vbox (badness 1484) has occurred while \output is active [3520] Overfull \hbox (8.8567pt too wide) in paragraph at lines 10761--10763 []\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 10763--10765 []\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 10771--10773 []\T1/pcr/m/n/10 is.infinite,nsparseVector-method Underfull \vbox (badness 1117) has occurred while \output is active [3521] Overfull \hbox (2.8567pt too wide) in paragraph at lines 10906--10908 []\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10912--10914 []\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 10914--10916 []\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method [3522] Overfull \hbox (8.8567pt too wide) in paragraph at lines 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[]\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method [3523] Overfull \hbox (20.8567pt too wide) in paragraph at lines 11089--11091 []\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11093--11095 []\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11095--11097 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11097--11099 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 11099--11101 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 11101--11103 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11103--11105 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11105--11107 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11107--11109 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 11109--11111 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 11113--11115 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11115--11117 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11117--11119 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11119--11121 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11121--11123 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method Underfull \vbox (badness 1117) has occurred while \output is active [3524] [3525] [3526] Overfull \hbox (50.8567pt too wide) in paragraph at lines 11578--11580 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11584--11586 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11586--11588 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11588--11590 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11590--11592 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11592--11594 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11598--11600 []\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11608--11610 []\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11610--11612 []\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 11612--11614 []\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 11614--11616 []\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 11616--11618 []\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method Underfull \vbox (badness 2903) has occurred while \output is active [3527] Overfull \hbox (2.8567pt too wide) in paragraph at lines 11624--11626 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11634--11636 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 11636--11638 []\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11644--11646 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11646--11648 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11648--11650 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 11650--11652 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11652--11654 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method Underfull \vbox (badness 3302) has occurred while \output is active [3528] [3529] [3530] [3531] Overfull \hbox (52.01662pt too wide) in paragraph at lines 12279--12281 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3532] [3533] [3534] Overfull \hbox (8.8567pt too wide) in paragraph at lines 12604--12606 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 12616--12618 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 12618--12620 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12624--12626 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 12642--12644 []\T1/pcr/m/n/10 norm,ldenseMatrix,character-method Underfull \vbox (badness 1824) has occurred while \output is active Overfull \hbox (14.8567pt too wide) in paragraph at lines 12648--12650 []\T1/pcr/m/n/10 norm,ndenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 12650--12652 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3535] Overfull \hbox (26.8567pt too wide) in paragraph at lines 12826--12828 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method [3536] Overfull \hbox (20.8567pt too wide) in paragraph at lines 12832--12834 []\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12844--12846 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 12846--12848 []\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 12848--12850 []\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12850--12852 []\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 12852--12854 []\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active Overfull \hbox (38.8567pt too wide) in paragraph at lines 12872--12874 []\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12874--12876 []\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12890--12892 []\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12910--12912 []\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method Underfull \vbox (badness 5847) has occurred while \output is active [3537] Overfull \hbox (38.8567pt too wide) in paragraph at lines 12912--12914 []\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12932--12934 []\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12940--12942 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12944--12946 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12946--12948 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 12948--12950 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Underfull \vbox (badness 4328) has occurred while \output is active Overfull \hbox (8.8567pt too wide) in paragraph at lines 12968--12970 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12970--12972 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 12972--12974 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 12974--12976 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12978--12980 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12982--12984 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12986--12988 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3538] Overfull \hbox (46.01662pt too wide) in paragraph at lines 13092--13094 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 13112--13114 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3539] [3540] [3541] [3542] [3543] [3544] Overfull \hbox (46.01662pt too wide) in paragraph at lines 13936--13938 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13939--13941 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13941--13943 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13943--13945 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13945--13947 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13947--13949 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 13949--13951 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13951--13953 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 13953--13955 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13955--13957 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 13959--13961 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13961--13963 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13963--13965 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13965--13967 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13967--13969 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 13969--13971 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3545] Underfull \vbox (badness 3769) has occurred while \output is active [3546] Overfull \hbox (4.01662pt too wide) in paragraph at lines 14205--14207 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 14274--14276 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3547] [3548] [3549] Overfull \hbox (26.8567pt too wide) in paragraph at lines 14660--14662 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14669--14671 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14671--14673 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14673--14675 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14675--14677 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 14685--14687 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 14694--14696 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method [3550] Overfull \hbox (32.8567pt too wide) in paragraph at lines 14708--14710 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14714--14716 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3551] Overfull \hbox (26.8567pt too wide) in paragraph at lines 14956--14958 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14958--14960 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14960--14962 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14962--14964 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 14966--14968 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14968--14970 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14970--14972 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14972--14974 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 14974--14976 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14976--14978 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14978--14980 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14984--14986 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Underfull \vbox (badness 2564) has occurred while \output is active [3552] Overfull \hbox (2.8567pt too wide) in paragraph at lines 14988--14990 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14998--15000 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15002--15004 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15004--15006 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15006--15008 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 15008--15010 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15010--15012 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15012--15014 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 15014--15016 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15040--15042 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15042--15044 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15044--15046 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15046--15048 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15050--15052 []\T1/pcr/m/n/10 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rcond,sparseMatrix,character-method [3553] Underfull \vbox (badness 1484) has occurred while \output is active [3554] [3555] [3556] [3557] Overfull \hbox (20.8567pt too wide) in paragraph at lines 15738--15740 []\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15740--15742 []\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15744--15746 []\T1/pcr/m/n/10 Schur,generalMatrix,logical-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 15746--15748 []\T1/pcr/m/n/10 Schur,generalMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15752--15754 []\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15754--15756 []\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 15756--15758 []\T1/pcr/m/n/10 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replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc} Output written on fullrefman.pdf (3634 pages, 9563211 bytes). Transcript written on fullrefman.log. make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc/manual' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/doc' make: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3' + exit 0 Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.72353 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + /bin/chmod -Rf u+rwX -- /usr/src/tmp/R-base-buildroot + : + /bin/rm -rf -- /usr/src/tmp/R-base-buildroot + cd R-3.4.3 + make 'INSTALL=/bin/install -p' install DESTDIR=/usr/src/tmp/R-base-buildroot install-pdf install-info make: Entering directory `/usr/src/RPM/BUILD/R-3.4.3' mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/m4' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/m4' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tools' make[1]: Nothing to be done for `install'. make[1]: Leaving directory 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'./usr/lib64/R/modules/R_X11.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/lapack.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/internet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) Verifying and fixing files in /usr/src/tmp/R-base-buildroot (binconfig,pkgconfig,libtool,desktop) /usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -L${rlibdir} -lR' Compressing files in /usr/src/tmp/R-base-buildroot (auto) Verifying info files in /usr/src/tmp/R-base-buildroot/usr/share/info (normal) Adjusting library links in /usr/src/tmp/R-base-buildroot ./usr/lib64: libR.so -> libR.so ./usr/lib64/R/lib: Verifying ELF objects in /usr/src/tmp/R-base-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal) Hardlinking identical .pyc and .opt-?.pyc files Hardlinking identical .pyc and .pyo files Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.88029 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.4.3 + export TZ= + TZ= + make check make: Entering directory `/usr/src/RPM/BUILD/R-3.4.3' make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests/Examples' Testing examples for package 'base' Testing examples for package 'tools' comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK Testing examples for package 'utils' Testing examples for package 'grDevices' comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK Testing examples for package 'graphics' comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK Testing examples for package 'stats' comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE 6564c6564 < Grand Mean: 291.5937 --- > Grand Mean: 291.5938 14989c14989 < Grand Mean: 291.5937 --- > Grand Mean: 291.5938 Testing examples for package 'datasets' comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK Testing examples for package 'methods' Testing examples for package 'grid' comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK Testing examples for package 'splines' comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK Testing examples for package 'stats4' comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK Testing examples for package 'tcltk' Testing examples for package 'compiler' Testing examples for package 'parallel' make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests/Examples' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running strict specific tests make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'any-all.R' ... OK comparing 'any-all.Rout' to './any-all.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ... OK comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running sloppy specific tests make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'print-tests.R' ... OK comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK running code in 'lapack.R' ... OK comparing 'lapack.Rout' to './lapack.Rout.save' ... OK running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK running code in 'datetime.R' ... OK comparing 'datetime.Rout' to './datetime.Rout.save' ... OK running code in 'iec60559.R' ... OK comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running regression tests ... make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running code in 'array-subset.R' ... OK running code in 'reg-tests-1a.R' ... OK running code in 'reg-tests-1b.R' ... OK running code in 'reg-tests-1c.R' ... OK running code in 'reg-tests-1d.R' ... OK running code in 'reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ... OK running code in 'p-qbeta-strict-tst.R' ... OK running code in 'r-strict-tst.R' ... OK running code in 'reg-IO.R' ... OK comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK running code in 'reg-IO2.R' ... OK comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK running code in 'reg-plot.R' ... OK comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK running code in 'reg-S4-examples.R' ... OK running code in 'reg-BLAS.R' ... OK make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running code in 'reg-tests-3.R' ... OK comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK running code in 'reg-examples3.R' ... OK comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ...326c326 < Achieved convergence tolerance: 9.33e-07 --- > Achieved convergence tolerance: 9.32e-07 393c393 < Achieved convergence tolerance: 2.15e-06 --- > Achieved convergence tolerance: 2.17e-06 OK running tests of plotting Latin-1 expect failure or some differences if not in a Latin-1 or UTF-8 locale running code in 'reg-plot-latin1.R' ... FAILED running code in 'reg-S4.R' ... OK comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running tests of Internet functions make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.4.3/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [2] "" > [3] "" > [4] "" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "" > [23] "" > > close(zz) > > > > # and via read.table, test http and ftp. > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3/tests' make: Leaving directory `/usr/src/RPM/BUILD/R-3.4.3' + exit 0 Processing files: R-base-3.4.3-alt0.M80P.1 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.53383 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.4.3 + DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.4.3 + export DOCDIR + rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.4.3 + /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.4.3 + cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.4.3 + chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.4.3 + chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.4.3 + exit 0 warning: File listed twice: /usr/lib64/R/library/KernSmooth/html warning: File listed twice: 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/usr/lib64/R/library/utils/html/browseURL.html warning: File listed twice: /usr/lib64/R/library/utils/html/browseVignettes.html warning: File listed twice: /usr/lib64/R/library/utils/html/bug.report.html warning: File listed twice: /usr/lib64/R/library/utils/html/capture.output.html warning: File listed twice: /usr/lib64/R/library/utils/html/changedFiles.html warning: File listed twice: /usr/lib64/R/library/utils/html/chooseBioCmirror.html warning: File listed twice: /usr/lib64/R/library/utils/html/chooseCRANmirror.html warning: File listed twice: /usr/lib64/R/library/utils/html/citEntry.html warning: File listed twice: /usr/lib64/R/library/utils/html/citation.html warning: File listed twice: /usr/lib64/R/library/utils/html/cite.html warning: File listed twice: /usr/lib64/R/library/utils/html/close.socket.html warning: File listed twice: /usr/lib64/R/library/utils/html/combn.html warning: File listed twice: /usr/lib64/R/library/utils/html/compareVersion.html warning: File listed twice: /usr/lib64/R/library/utils/html/contrib.url.html warning: File listed twice: /usr/lib64/R/library/utils/html/count.fields.html warning: File listed twice: /usr/lib64/R/library/utils/html/create.post.html warning: File listed twice: /usr/lib64/R/library/utils/html/data.html warning: File listed twice: /usr/lib64/R/library/utils/html/dataentry.html warning: File listed twice: /usr/lib64/R/library/utils/html/debugcall.html warning: File listed twice: /usr/lib64/R/library/utils/html/debugger.html warning: File listed twice: /usr/lib64/R/library/utils/html/demo.html warning: File listed twice: /usr/lib64/R/library/utils/html/download.file.html warning: File listed twice: /usr/lib64/R/library/utils/html/download.packages.html warning: File listed twice: /usr/lib64/R/library/utils/html/edit.data.frame.html warning: File listed twice: /usr/lib64/R/library/utils/html/edit.html warning: File listed twice: /usr/lib64/R/library/utils/html/example.html warning: File listed twice: /usr/lib64/R/library/utils/html/file.edit.html warning: File listed twice: /usr/lib64/R/library/utils/html/filetest.html warning: File listed twice: /usr/lib64/R/library/utils/html/findLineNum.html warning: File listed twice: /usr/lib64/R/library/utils/html/fix.html warning: File listed twice: /usr/lib64/R/library/utils/html/flush.console.html warning: File listed twice: /usr/lib64/R/library/utils/html/format.html warning: File listed twice: /usr/lib64/R/library/utils/html/getAnywhere.html warning: File listed twice: /usr/lib64/R/library/utils/html/getFromNamespace.html warning: File listed twice: /usr/lib64/R/library/utils/html/getParseData.html warning: File listed twice: /usr/lib64/R/library/utils/html/getS3method.html warning: File listed twice: /usr/lib64/R/library/utils/html/glob2rx.html warning: File listed twice: /usr/lib64/R/library/utils/html/globalVariables.html warning: File listed twice: /usr/lib64/R/library/utils/html/hasName.html warning: File listed twice: /usr/lib64/R/library/utils/html/head.html warning: File listed twice: /usr/lib64/R/library/utils/html/help.html warning: File listed twice: /usr/lib64/R/library/utils/html/help.request.html warning: File listed twice: /usr/lib64/R/library/utils/html/help.search.html warning: File listed twice: /usr/lib64/R/library/utils/html/help.start.html warning: File listed twice: /usr/lib64/R/library/utils/html/hsearch-utils.html warning: File listed twice: /usr/lib64/R/library/utils/html/install.packages.html warning: File listed twice: /usr/lib64/R/library/utils/html/installed.packages.html warning: File listed twice: /usr/lib64/R/library/utils/html/isS3method.html warning: File listed twice: /usr/lib64/R/library/utils/html/isS3stdGen.html warning: File listed twice: /usr/lib64/R/library/utils/html/localeToCharset.html warning: File listed twice: /usr/lib64/R/library/utils/html/ls_str.html warning: File listed twice: /usr/lib64/R/library/utils/html/maintainer.html warning: File listed twice: /usr/lib64/R/library/utils/html/make.packages.html.html warning: File listed twice: /usr/lib64/R/library/utils/html/make.socket.html warning: File listed twice: /usr/lib64/R/library/utils/html/memory.size.html warning: File listed twice: /usr/lib64/R/library/utils/html/menu.html warning: File listed twice: /usr/lib64/R/library/utils/html/methods.html warning: File listed twice: /usr/lib64/R/library/utils/html/mirrorAdmin.html warning: File listed twice: /usr/lib64/R/library/utils/html/modifyList.html warning: File listed twice: /usr/lib64/R/library/utils/html/news.html warning: File listed twice: /usr/lib64/R/library/utils/html/nsl.html warning: File listed twice: /usr/lib64/R/library/utils/html/object.size.html warning: File listed twice: /usr/lib64/R/library/utils/html/package.skeleton.html warning: File listed twice: /usr/lib64/R/library/utils/html/packageDescription.html warning: File listed twice: /usr/lib64/R/library/utils/html/packageName.html warning: File listed twice: /usr/lib64/R/library/utils/html/packageStatus.html warning: File listed twice: /usr/lib64/R/library/utils/html/page.html warning: File listed twice: /usr/lib64/R/library/utils/html/person.html warning: File listed twice: /usr/lib64/R/library/utils/html/process.events.html warning: File listed twice: /usr/lib64/R/library/utils/html/prompt.html warning: File listed twice: /usr/lib64/R/library/utils/html/promptData.html warning: File listed twice: /usr/lib64/R/library/utils/html/promptPackage.html warning: File listed twice: /usr/lib64/R/library/utils/html/rcompgen.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.DIF.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.fortran.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.fwf.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.socket.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.table.html warning: File listed twice: /usr/lib64/R/library/utils/html/recover.html warning: File listed twice: /usr/lib64/R/library/utils/html/relist.html warning: File listed twice: /usr/lib64/R/library/utils/html/remove.packages.html warning: File listed twice: /usr/lib64/R/library/utils/html/removeSource.html warning: File listed twice: /usr/lib64/R/library/utils/html/roman.html warning: File listed twice: /usr/lib64/R/library/utils/html/rtags.html warning: File listed twice: /usr/lib64/R/library/utils/html/savehistory.html warning: File listed twice: /usr/lib64/R/library/utils/html/select.list.html warning: File listed twice: /usr/lib64/R/library/utils/html/sessionInfo.html warning: File listed twice: /usr/lib64/R/library/utils/html/setRepositories.html warning: File listed twice: /usr/lib64/R/library/utils/html/sourceutils.html warning: File listed twice: /usr/lib64/R/library/utils/html/stack.html warning: File listed twice: /usr/lib64/R/library/utils/html/str.html warning: File listed twice: /usr/lib64/R/library/utils/html/strcapture.html warning: File listed twice: /usr/lib64/R/library/utils/html/summaryRprof.html warning: File listed twice: /usr/lib64/R/library/utils/html/tar.html warning: File listed twice: /usr/lib64/R/library/utils/html/toLatex.html warning: File listed twice: /usr/lib64/R/library/utils/html/txtProgressBar.html warning: File listed twice: /usr/lib64/R/library/utils/html/type.convert.html warning: File listed twice: /usr/lib64/R/library/utils/html/untar.html warning: File listed twice: /usr/lib64/R/library/utils/html/unzip.html warning: File listed twice: /usr/lib64/R/library/utils/html/update.packages.html warning: File listed twice: /usr/lib64/R/library/utils/html/url.show.html warning: File listed twice: /usr/lib64/R/library/utils/html/utils-defunct.html warning: File listed twice: /usr/lib64/R/library/utils/html/utils-deprecated.html warning: File listed twice: /usr/lib64/R/library/utils/html/utils-package.html warning: File listed twice: /usr/lib64/R/library/utils/html/vignette.html warning: File listed twice: /usr/lib64/R/library/utils/html/write.table.html warning: File listed twice: /usr/lib64/R/library/utils/html/zip.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.oeTvzf find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) lib.prov: /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so: 1063 symbols, 21 bpp ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' --- find-provides-deps 2019-04-21 04:24:36.852956425 +0000 +++ filter-provides-deps 2019-04-21 04:24:36.853956432 +0000 @@ -1 +1,2 @@ libR.so()(64bit) = set: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 +libR-2.11.so()(64bit) = set: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 Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.HlLFPh find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,tcl,typelib) lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/MASS/libs/MASS.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/foreign/libs/foreign.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grDevices/libs/grDevices.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/graphics/libs/graphics.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grid/libs/grid.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/lattice/libs/lattice.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/nnet/libs/nnet.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/rpart/libs/rpart.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/spatial/libs/spatial.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/survival/libs/survival.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/utils/libs/utils.so: underlinked libraries: /lib64/liblzma.so.5 /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules/internet.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules/lapack.so: underlinked libraries: /lib64/libdl.so.2 shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh/echo.sh is not executable find-requires: FINDPACKAGE-COMMANDS: cat grep sh Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set: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 Requires: /bin/sh, /lib64/ld-linux-x86-64.so.2, coreutils, grep, ld-linux-x86-64.so.2()(64bit) >= set:ihbW3, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426Dgj994wsONU8RZq4ZjETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQZtURAFElDl8totXyLZkjPS80tH2, libXmu.so.6()(64bit) >= set:ljat5WdZ0, libXt.so.6()(64bit) >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1()(64bit) >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJLac4, libc.so.6(GLIBC_2.11)(64bit), libc.so.6(GLIBC_2.14)(64bit), libc.so.6(GLIBC_2.15)(64bit), libc.so.6(GLIBC_2.16)(64bit), libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libc.so.6(GLIBC_2.6)(64bit), libc.so.6(GLIBC_2.7)(64bit), libc.so.6(GLIBC_2.8)(64bit), libcairo.so.2()(64bit) >= set:mgBeCp25NOIyrlQHFsTG1phW01upHNOW8SpbeVohC5Pwchq6KplkgZIPAQh02Zr5HMxPMkimVZpVN9h6QFUdKO6OFjNsjitz641ARaZ5HZAmxdD86kgBnSaNq3ZAVlemZpcoP0tsFeDiZfuQuf3, libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, libdl.so.2(GLIBC_2.2.5)(64bit), libgobject-2.0.so.0()(64bit) >= set:ml6W90, libicui18n.so.56()(64bit) >= set:qnGSBTabJaKTA5iRNI1fbGkb, libicuuc.so.56()(64bit) >= set:pmZp9FuftEXt5chG0, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQ6Ly73P71OXgQjXcEVpBpZdQN0du6bEemIGcwvkRUyfGzE7kPRWTAeHIPYhIl5WiNVlN8FgR6mScaXXLmW0FDbvWuDSCea0aj0BvFxRc15QVQjV9n85Kyco0a0SzG6SwK1cfwAyHaix50g7p00c0WMF2, liblzma.so.5()(64bit) >= set:kgIy0DJdgZuHF5yXYppdmYIDYAa1, liblzma.so.5(XZ_5.0)(64bit), libm.so.6(GLIBC_2.2.5)(64bit), libm.so.6(GLIBC_2.23)(64bit), libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQ6cD75j31i4ky6SMMCoRQ1, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre.so.3()(64bit) >= set:ieELhsZ4oFM1uTpGS8bAqz69j4, libpng15.so.15()(64bit) >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng15.so.15(PNG15_0)(64bit), libreadline.so.6()(64bit) >= set:nidQ8PMktsCwid18OsyEUS8ifZzElko8gle73YghFZmboE0sZwI3SqZmUftG8A4bFXX0BVGKnVqwyZw4mp, librt.so.1()(64bit) >= set:jiq20, librt.so.1(GLIBC_2.2.5)(64bit), libtiff.so.5()(64bit) >= set:lhyG9VP2iv3ttOWkLJhCwlrr, libz.so.1()(64bit) >= set:kgb6dgb5xDnazO8BhqfiJqdZd6eIL9, rtld(GNU_HASH), sh Requires(rpmlib): rpmlib(SetVersions) Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.OIKBjt Creating R-base-debuginfo package Processing files: R-devel-3.4.3-alt0.M80P.1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.z8ko6I find-provides: broken symbolic link /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool -> ../../../bin/libtool is not going to provide anything find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.Obs261 find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,tcl,typelib) /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header # error R_ext/GraphicsEngine.h must be included first, and includes this header ^ cpp.req: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed, trying c++ mode /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header # error R_ext/GraphicsEngine.h must be included first, and includes this header ^ cpp.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed find-requires: FINDPACKAGE-COMMANDS: chmod mkdir rm rmdir Provides: pkgconfig(libR) = 3.4.3 PreReq: R-base = 3.4.3-alt0.M80P.1 Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/libR.so, /usr/lib64/pkgconfig, coreutils Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.5Z0PTq Processing files: R-tcltk-3.4.3-alt0.M80P.1 warning: File listed twice: /usr/lib64/R/library/tcltk/html warning: File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/R.css warning: File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ScitTS find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ZBM1Zn find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,tcl,typelib) Provides: tcl(::Utility) = 1.0, tcl(::Utility::dump) = 1.0, tcl(::Utility::expand) = 1.0, tcl(::Utility::number) = 1.0, tcl(::Utility::string) = 1.0, tcl(::Utility::tk) = 1.0, tcl(Hierarchy) = 2.0, tcl(PBar) = 1.0, tcl(Widget) = 2.0 Requires: R-base = 3.4.3-alt0.M80P.1, libR.so()(64bit) >= set:oiZ4ZDvavd6WNT8RxhdprIL0xNSQjrGSanE12warZ61UkMZtzOOW0cQ6tLN8BjJrkKZnL1TE3fUmVTkIHiOQO1D71LZCEMTQx9TL6bQBPaZx0xbnGs2y0VRyIqwAj5wzR8tEB98b75EDoSl8X0IafvpnoMu0, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.5.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.5.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk) Requires(rpmlib): rpmlib(SetVersions) Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.gISF8V Creating R-tcltk-debuginfo package Processing files: R-doc-html-3.4.3-alt0.M80P.1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.dAsAqx find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.CK6p1b find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,tcl,typelib) Requires: R-base = 3.4.3-alt0.M80P.1 Processing files: R-doc-pdf-3.4.3-alt0.M80P.1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.7L0tRT find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.6a9GNE find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,tcl,typelib) Conflicts: R-base > 3.4.3, R-base < 3.4.3 Processing files: R-doc-info-3.4.3-alt0.M80P.1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.HJUfLs find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.qaaDMj find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,tcl,typelib) Conflicts: R-base > 3.4.3, R-base < 3.4.3 Processing files: R-base-debuginfo-3.4.3-alt0.M80P.1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.tnvd9d find-provides: running scripts (debuginfo) ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ks3UDb find-requires: running scripts (debuginfo) Provides: debug64(libR.so) Requires: R-base = 3.4.3-alt0.M80P.1, /usr/lib/debug/lib64/ld-linux-x86-64.so.2.debug, debug64(ld-linux-x86-64.so.2), debug64(libX11.so.6), debug64(libXmu.so.6), debug64(libXt.so.6), debug64(libbz2.so.1), debug64(libc.so.6), debug64(libcairo.so.2), debug64(libcurl.so.4), debug64(libdl.so.2), debug64(libgobject-2.0.so.0), debug64(libicui18n.so.56), debug64(libicuuc.so.56), debug64(libjpeg.so.62), debug64(liblapack.so.4), debug64(liblzma.so.5), debug64(libm.so.6), debug64(libopenblas.so.0), debug64(libpango-1.0.so.0), debug64(libpangocairo-1.0.so.0), debug64(libpcre.so.3), debug64(libpng15.so.15), debug64(libreadline.so.6), debug64(librt.so.1), debug64(libtiff.so.5), debug64(libz.so.1) Processing files: R-tcltk-debuginfo-3.4.3-alt0.M80P.1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.rdXu4j find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.aMq3Pv find-requires: running scripts (debuginfo) Requires: R-tcltk = 3.4.3-alt0.M80P.1, debug64(libR.so), debug64(libc.so.6), debug64(libtcl8.5.so), debug64(libtk8.5.so) Adding to R-tcltk-debuginfo a strict dependency on R-base-debuginfo Removing from R-tcltk-debuginfo 10 sources provided by R-base-debuginfo also prunning dir /usr/src/debug/R-3.4.3/src/include Removing 1 extra deps from R-devel due to dependency on R-base Removing 1 extra deps from R-tcltk due to dependency on R-base Removing 1 extra deps from R-tcltk-debuginfo due to dependency on R-base-debuginfo Removing 2 extra deps from R-devel due to repentancy on R-base Removing 5 extra deps from R-tcltk due to repentancy on R-base Removing 1 extra deps from R-tcltk-debuginfo due to repentancy on R-base-debuginfo warning: Installed (but unpackaged) file(s) found: /usr/lib64/R/COPYING /usr/lib64/R/SVN-REVISION /usr/lib64/R/library/translations/DESCRIPTION /usr/lib64/R/library/translations/da/LC_MESSAGES/R-base.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-compiler.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-grDevices.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-graphics.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-grid.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-methods.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-parallel.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-splines.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-stats.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-stats4.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-tcltk.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-tools.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R-utils.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/R.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/RGui.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/grDevices.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/graphics.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/grid.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/methods.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/parallel.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/splines.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/stats.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/tcltk.mo /usr/lib64/R/library/translations/da/LC_MESSAGES/tools.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-base.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-compiler.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-grDevices.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-graphics.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-grid.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-methods.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-parallel.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-splines.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-stats.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-stats4.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-tcltk.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-tools.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R-utils.mo /usr/lib64/R/library/translations/de/LC_MESSAGES/R.mo 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