<86>Sep 2 01:59:38 userdel[3252811]: delete user 'rooter'
<86>Sep 2 01:59:38 userdel[3252811]: removed group 'rooter' owned by 'rooter'
<86>Sep 2 01:59:38 userdel[3252811]: removed shadow group 'rooter' owned by 'rooter'
<86>Sep 2 01:59:38 groupadd[3252818]: group added to /etc/group: name=rooter, GID=1796
<86>Sep 2 01:59:38 groupadd[3252818]: group added to /etc/gshadow: name=rooter
<86>Sep 2 01:59:38 groupadd[3252818]: new group: name=rooter, GID=1796
<86>Sep 2 01:59:38 useradd[3252824]: new user: name=rooter, UID=1796, GID=1796, home=/root, shell=/bin/bash, from=none
<86>Sep 2 01:59:38 userdel[3252834]: delete user 'builder'
<86>Sep 2 01:59:38 userdel[3252834]: removed group 'builder' owned by 'builder'
<86>Sep 2 01:59:38 userdel[3252834]: removed shadow group 'builder' owned by 'builder'
<86>Sep 2 01:59:38 groupadd[3252841]: group added to /etc/group: name=builder, GID=1797
<86>Sep 2 01:59:38 groupadd[3252841]: group added to /etc/gshadow: name=builder
<86>Sep 2 01:59:38 groupadd[3252841]: new group: name=builder, GID=1797
<86>Sep 2 01:59:38 useradd[3252848]: new user: name=builder, UID=1797, GID=1797, home=/usr/src, shell=/bin/bash, from=none
warning: Macro %add_tcl_lib_path not found
<13>Sep 2 01:59:49 rpmi: xorg-proto-devel-2023.2-alt1 sisyphus+327257.100.1.1 1692178218 installed
<13>Sep 2 01:59:49 rpmi: libpng16-1.6.40-alt1 sisyphus+323732.100.1.1 1687771851 installed
<13>Sep 2 01:59:49 rpmi: libjpeg-2:2.1.2-alt1.2 sisyphus+300827.100.2.1 1653916633 installed
<13>Sep 2 01:59:49 rpmi: libexpat-2.5.0-alt1 sisyphus+309227.100.1.1 1667075764 installed
<13>Sep 2 01:59:49 rpmi: perl-HTTP-Date-6.06-alt1 sisyphus+324527.100.1.1 1688834564 installed
<13>Sep 2 01:59:49 rpmi: tex-common-0.2-alt4 sisyphus+276869.100.1.1 1625246366 installed
<13>Sep 2 01:59:49 rpmi: perl-Term-ANSIColor-5.01-alt1 sisyphus+244783.100.1.2 1579747505 installed
<13>Sep 2 01:59:49 rpmi: perl-Unicode-Normalize-1:5.34.1-alt1 sisyphus+303178.100.1.1 1656953516 installed
<13>Sep 2 01:59:49 rpmi: libidn2-2.3.4-alt1 sisyphus+309023.100.1.1 1666791084 installed
<13>Sep 2 01:59:49 rpmi: libnettle8-3.9.1-alt1 sisyphus+322548.100.1.2 1686176879 installed
<13>Sep 2 01:59:49 rpmi: less-633-alt1 sisyphus+328181.300.2.1 1693321749 installed
<13>Sep 2 01:59:49 rpmi: libICE-1.1.1-alt1 sisyphus+311428.500.1.1 1670577555 installed
<13>Sep 2 01:59:49 rpmi: libicu73-1:7.3.2-alt1 sisyphus+323036.100.1.1 1686763352 installed
<13>Sep 2 01:59:49 rpmi: libgraphite2-1.3.14-alt2.1 sisyphus+279571.100.1.2 1626605111 installed
<13>Sep 2 01:59:49 rpmi: libSM-1.2.4-alt1 sisyphus+312057.200.1.1 1671526916 installed
<13>Sep 2 01:59:49 rpmi: perl-Tie-RefHash-1.40-alt1 sisyphus+260329.100.1.1 1603548550 installed
<13>Sep 2 01:59:49 rpmi: perl-IO-Stringy-2.113-alt1 sisyphus+289915.300.2.1 1637124493 installed
<13>Sep 2 01:59:49 rpmi: perl-IO-Socket-IP-0.42-alt1 sisyphus+325815.100.1.2 1690571193 installed
<13>Sep 2 01:59:49 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed
<13>Sep 2 01:59:49 rpmi: perl-libnet-1:3.15-alt1 sisyphus+317310.100.1.1 1679580208 installed
<13>Sep 2 01:59:49 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed
<13>Sep 2 01:59:49 rpmi: perl-Compress-Raw-Zlib-2.206-alt1 sisyphus+325780.100.1.1 1690558898 installed
<13>Sep 2 01:59:49 rpmi: rpm-macros-info-install-6.7-alt1 sisyphus+328181.1400.3.1 1693325447 installed
<13>Sep 2 01:59:49 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed
<13>Sep 2 01:59:49 rpmi: libtcl-8.6.13-alt1 sisyphus+310696.100.1.1 1669548266 installed
<13>Sep 2 01:59:49 rpmi: tcl-8.6.13-alt1 sisyphus+310696.100.1.1 1669548266 installed
<13>Sep 2 01:59:49 rpmi: libopenblas-0.3.23-alt1.2 sisyphus+325749.100.1.1 1690531809 installed
<13>Sep 2 01:59:49 rpmi: javapackages-filesystem-1:6.0.0-alt2_7jpp11 sisyphus+318644.100.1.1 1681742255 installed
<13>Sep 2 01:59:49 rpmi: libxxhash-0.8.0-alt2 sisyphus+277476.100.2.1 1625621312 installed
<13>Sep 2 01:59:49 rpmi: libwebp7-1.3.1-alt1 sisyphus+323891.100.1.1 1688040826 installed
<13>Sep 2 01:59:49 rpmi: liblz4-1:1.9.4-alt1 sisyphus+309416.100.1.1 1667412981 installed
<13>Sep 2 01:59:49 rpmi: libquadmath0-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:49 rpmi: libgfortran5-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:50 rpmi: libpixman-3:0.42.2-alt1 sisyphus+309549.100.1.1 1667649219 installed
<13>Sep 2 01:59:50 rpmi: libbrotlicommon-1.1.0-alt1 sisyphus+328501.100.1.1 1693598419 installed
<13>Sep 2 01:59:50 rpmi: libbrotlidec-1.1.0-alt1 sisyphus+328501.100.1.1 1693598419 installed
<13>Sep 2 01:59:50 rpmi: libharfbuzz-8.1.1-alt1 sisyphus+326343.100.1.1 1691060130 installed
<13>Sep 2 01:59:50 rpmi: libfreetype-2.13.1-alt1 sisyphus+324353.100.1.1 1688638057 installed
<13>Sep 2 01:59:50 rpmi: libfontconfig1-2.14.2-alt8 sisyphus+328444.100.1.1 1693553402 installed
<13>Sep 2 01:59:50 rpmi: libbrotlienc-1.1.0-alt1 sisyphus+328501.100.1.1 1693598419 installed
<13>Sep 2 01:59:50 rpmi: zlib-devel-1.2.13-alt1 sisyphus+309409.200.2.1 1667402043 installed
<13>Sep 2 01:59:50 rpmi: libXau-1.0.11-alt1 sisyphus+311428.100.1.1 1670577439 installed
<13>Sep 2 01:59:50 rpmi: libgdbm-1.8.3-alt10 sisyphus+278100.1600.1.1 1626058413 installed
<13>Sep 2 01:59:50 rpmi: xml-utils-1:2.10.4-alt1 sisyphus+311250.4140.175.1 1685628991 installed
<13>Sep 2 01:59:50 rpmi: fontconfig-2.14.2-alt8 sisyphus+328444.100.1.1 1693553402 installed
Updating fonts cache: <29>Sep 2 01:59:51 fontconfig: Updating fonts cache: succeeded
[ DONE ]
<13>Sep 2 01:59:51 rpmi: libp11-kit-1:0.24.1-alt2 sisyphus+324666.100.1.1 1689083439 installed
<13>Sep 2 01:59:51 rpmi: libtasn1-4.19.0-alt3 sisyphus+327816.100.1.1 1692802615 installed
<13>Sep 2 01:59:51 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed
<13>Sep 2 01:59:51 rpmi: rpm-build-gir-0.7.3-alt3.1 sisyphus+319393.100.1.1 1682538783 installed
<13>Sep 2 01:59:51 rpmi: libXau-devel-1.0.11-alt1 sisyphus+311428.100.1.1 1670577439 installed
<13>Sep 2 01:59:51 rpmi: libpng-devel-1.6.40-alt1 sisyphus+323732.100.1.1 1687771851 installed
<13>Sep 2 01:59:51 rpmi: libwoff2-1.0.2-alt3 sisyphus+302729.100.1.1 1656351540 installed
<13>Sep 2 01:59:51 rpmi: libharfbuzz-icu-8.1.1-alt1 sisyphus+326343.100.1.1 1691060130 installed
<13>Sep 2 01:59:51 rpmi: libharfbuzz-gobject-8.1.1-alt1 sisyphus+326343.100.1.1 1691060130 installed
<13>Sep 2 01:59:51 rpmi: libquadmath13-devel-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:51 rpmi: libsystemd-1:253.8-alt1 sisyphus+326901.100.1.1 1691693037 installed
<13>Sep 2 01:59:51 rpmi: libdbus-1.14.8-alt1 sisyphus+324298.100.1.1 1688559488 installed
<13>Sep 2 01:59:51 rpmi: libavahi-0.8-alt2 sisyphus+321176.300.10.2 1684802422 installed
<13>Sep 2 01:59:51 rpmi: javapackages-tools-1:6.0.0-alt2_7jpp11 sisyphus+318644.100.1.1 1681742255 installed
<13>Sep 2 01:59:51 rpmi: java-common-1.6.0-alt1 sisyphus+234020.100.1.1 1562437039 installed
<13>Sep 2 01:59:51 rpmi: libopenblas-devel-0.3.23-alt1.2 sisyphus+325749.100.1.1 1690531809 installed
<13>Sep 2 01:59:51 rpmi: perl-OLE-Storage_Lite-0.22-alt1 sisyphus+315433.100.1.1 1676717427 installed
<13>Sep 2 01:59:51 rpmi: perl-autodie-2.36-alt1 sisyphus+314475.100.1.1 1675194557 installed
<13>Sep 2 01:59:51 rpmi: libgraphite2-devel-1.3.14-alt2.1 sisyphus+279571.100.1.2 1626605111 installed
<13>Sep 2 01:59:51 rpmi: icu-utils-1:7.3.2-alt1 sisyphus+323036.100.1.1 1686763352 installed
<13>Sep 2 01:59:51 rpmi: libicu-devel-1:7.3.2-alt1 sisyphus+323036.100.1.1 1686763352 installed
<13>Sep 2 01:59:51 rpmi: libICE-devel-1.1.1-alt1 sisyphus+311428.500.1.1 1670577555 installed
<13>Sep 2 01:59:51 rpmi: libSM-devel-1.2.4-alt1 sisyphus+312057.200.1.1 1671526916 installed
<13>Sep 2 01:59:51 rpmi: libhogweed6-3.9.1-alt1 sisyphus+322548.100.1.2 1686176879 installed
<13>Sep 2 01:59:51 rpmi: libgnutls30-3.8.1-alt2 sisyphus+326772.40.3.1 1692114175 installed
<13>Sep 2 01:59:51 rpmi: libngtcp2.13-0.16.0-alt1 sisyphus+323677.40.3.1 1687690555 installed
<13>Sep 2 01:59:51 rpmi: libngtcp2_crypto_gnutls5-0.16.0-alt1 sisyphus+323677.40.3.1 1687690555 installed
<13>Sep 2 01:59:51 rpmi: perl-unicore-1:5.34.1-alt1 sisyphus+303178.100.1.1 1656953516 installed
<13>Sep 2 01:59:51 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+279723.3100.1.1 1626649600 installed
<13>Sep 2 01:59:51 rpmi: perl-Data-Dump-1.25-alt1 sisyphus+276551.100.1.1 1625126880 installed
<13>Sep 2 01:59:51 rpmi: perl-File-Listing-6.16-alt1 sisyphus+325783.100.1.1 1690559356 installed
<13>Sep 2 01:59:51 rpmi: groff-base-1.22.3-alt2 sisyphus+275306.100.2.1 1624538375 installed
<13>Sep 2 01:59:51 rpmi: zziplib-0.13.72-alt1 sisyphus+278032.100.1.2 1625982008 installed
<13>Sep 2 01:59:51 rpmi: t1utils-1.42-alt1 sisyphus+278458.100.1.1 1626102085 installed
<13>Sep 2 01:59:51 rpmi: ttf2pt1-3.4.4-alt1.qa1 sisyphus+275192.100.2.1 1624905844 installed
<13>Sep 2 01:59:51 rpmi: rpm-build-tcl-0.6.2-alt1 sisyphus+299320.100.1.1 1651401392 installed
<13>Sep 2 01:59:51 rpmi: tcl-devel-8.6.13-alt1 sisyphus+310696.100.1.1 1669548266 installed
<13>Sep 2 01:59:51 rpmi: perl-X11-Protocol-0.56-alt1.1 1290621401 installed
<13>Sep 2 01:59:51 rpmi: perl-TimeDate-2.33-alt1 sisyphus+252901.100.1.1 1591387378 installed
<13>Sep 2 01:59:51 rpmi: perl-Unicode-Map-0.112-alt8 sisyphus+279723.3600.1.1 1626649989 installed
<13>Sep 2 01:59:51 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed
<13>Sep 2 01:59:51 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed
<13>Sep 2 01:59:51 rpmi: perl-IPC-System-Simple-1.30-alt1 sisyphus+248544.100.1.1 1585154078 installed
<13>Sep 2 01:59:51 rpmi: perl-IPC-Run3-0.048-alt1 1410690027 installed
<13>Sep 2 01:59:51 rpmi: psutils-2:2.07-alt1 sisyphus+299224.700.1.1 1651226336 installed
<13>Sep 2 01:59:51 rpmi: perl-Try-Tiny-0.31-alt1 sisyphus+290597.100.1.1 1637915507 installed
<13>Sep 2 01:59:51 rpmi: perl-Module-Load-0.36-alt1 sisyphus+258992.100.1.1 1601543407 installed
<13>Sep 2 01:59:51 rpmi: perl-IO-Compress-Brotli-2:0.004001-alt3 sisyphus+302124.100.1.1 1655283093 installed
<13>Sep 2 01:59:51 rpmi: perl-File-Which-1.27-alt1 sisyphus+271986.100.1.1 1621196035 installed
<13>Sep 2 01:59:51 rpmi: perl-File-Copy-Recursive-0.45-alt1 sisyphus+235291.100.1.1 1564606222 installed
<13>Sep 2 01:59:51 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+279723.3400.1.1 1626649913 installed
<13>Sep 2 01:59:51 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed
<13>Sep 2 01:59:51 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed
<13>Sep 2 01:59:51 rpmi: perl-Clone-0.46-alt1 sisyphus+308850.100.1.3 1666451819 installed
<13>Sep 2 01:59:51 rpmi: perl-Term-Cap-1.18-alt1 sisyphus+315126.100.1.1 1676227129 installed
<13>Sep 2 01:59:51 rpmi: perl-IO-String-1.08-alt2 1321677915 installed
<13>Sep 2 01:59:51 rpmi: perl-Compress-Raw-Bzip2-2.206-alt1 sisyphus+325779.100.1.1 1690558767 installed
<13>Sep 2 01:59:51 rpmi: perl-Algorithm-Diff-1:1.201-alt1 sisyphus+263447.100.1.1 1607956595 installed
<13>Sep 2 01:59:51 rpmi: perl-Unicode-EastAsianWidth-12.0-alt1 sisyphus+237401.100.1.1 1568197363 installed
<13>Sep 2 01:59:51 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed
<13>Sep 2 01:59:51 rpmi: perl-Filter-1.64-alt1 sisyphus+305464.100.1.1 1660815327 installed
<13>Sep 2 01:59:51 rpmi: perl-Encode-3.19-alt1 sisyphus+304776.100.1.1 1659623409 installed
<13>Sep 2 01:59:51 rpmi: perl-URI-5.21-alt1 sisyphus+327918.100.1.1 1692972838 installed
<13>Sep 2 01:59:51 rpmi: perl-IO-Compress-2.206-alt1 sisyphus+325819.100.1.1 1690563199 installed
<13>Sep 2 01:59:51 rpmi: perl-HTML-Parser-3.81-alt1 sisyphus+314462.100.1.1 1675193797 installed
<13>Sep 2 01:59:51 rpmi: perl-Net-HTTP-6.23-alt1 sisyphus+323470.100.1.1 1687422469 installed
<13>Sep 2 01:59:51 rpmi: perl-Pod-Simple-3.45-alt1 sisyphus+321554.100.1.1 1684663135 installed
<13>Sep 2 01:59:51 rpmi: perl-Pod-Usage-2.03-alt1 sisyphus+300436.100.1.3 1653292807 installed
<13>Sep 2 01:59:51 rpmi: perl-podlators-5.01-alt1 sisyphus+312638.100.1.1 1672339228 installed
<13>Sep 2 01:59:51 rpmi: perl-IO-Zlib-1.14-alt1 sisyphus+313249.100.1.1 1673493698 installed
<13>Sep 2 01:59:51 rpmi: perl-Archive-Tar-3.02-alt1 sisyphus+318647.100.1.1 1681742479 installed
<13>Sep 2 01:59:51 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed
<13>Sep 2 01:59:51 rpmi: perl-libintl-1.33-alt1.1 sisyphus+312319.100.1.1 1671854214 installed
<13>Sep 2 01:59:51 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed
<13>Sep 2 01:59:51 rpmi: perl-IO-HTML-1.004-alt1 sisyphus+258983.100.1.1 1601542619 installed
<13>Sep 2 01:59:51 rpmi: perl-HTTP-Message-6.44-alt1 sisyphus+309106.100.1.1 1666913573 installed
<13>Sep 2 01:59:51 rpmi: perl-HTML-Form-6.11-alt1 sisyphus+315122.100.1.1 1676226686 installed
<13>Sep 2 01:59:51 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed
<13>Sep 2 01:59:51 rpmi: perl-libwww-6.72-alt1 sisyphus+325791.100.1.2 1690563984 installed
<13>Sep 2 01:59:51 rpmi: perl-HTML-Tree-5.07-alt1 sisyphus+277105.100.1.1 1625402682 installed
<13>Sep 2 01:59:51 rpmi: perl-HTML-Formatter-2.16-alt2 sisyphus+306600.100.1.1 1663005434 installed
<13>Sep 2 01:59:51 rpmi: perl-XML-Parser-2.46-alt1 sisyphus+279723.1300.1.1 1626649131 installed
<13>Sep 2 01:59:51 rpmi: perl-XML-Twig-3.52-alt1 sisyphus+277116.100.1.2 1625410693 installed
<13>Sep 2 01:59:51 rpmi: perl-Net-DBus-1.2.0-alt1 sisyphus+279723.2700.1.1 1626649518 installed
<13>Sep 2 01:59:51 rpmi: perl-XML-XPath-1.48-alt1 sisyphus+305097.100.1.2 1660226797 installed
<13>Sep 2 01:59:51 rpmi: perl-HTTP-Cookies-6.10-alt1 sisyphus+264349.100.1.1 1609891183 installed
<13>Sep 2 01:59:51 rpmi: perl-WWW-Mechanize-2.17-alt2 sisyphus+327930.100.1.1 1692978437 installed
<13>Sep 2 01:59:51 rpmi: perl-Text-CSV_XS-1.51-alt1 sisyphus+327117.100.1.1 1691932336 installed
<13>Sep 2 01:59:51 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed
<13>Sep 2 01:59:51 rpmi: lua5.3-5.3.6-alt3 sisyphus+302797.276.28.1 1657376706 installed
<13>Sep 2 01:59:51 rpmi: libtre5-0.8.0-alt2.2 sisyphus+278356.100.1.1 1626091408 installed
<13>Sep 2 01:59:51 rpmi: libtexlua5-2021-alt5_3 sisyphus+325758.20.3.1 1690546231 installed
<13>Sep 2 01:59:51 rpmi: libteckit-2.5.1-alt2.1 sisyphus+275250.100.2.1 1624906328 installed
<13>Sep 2 01:59:51 rpmi: libteckit-utils-2.5.1-alt2.1 sisyphus+275250.100.2.1 1624906328 installed
<13>Sep 2 01:59:51 rpmi: libsynctex2-2021-alt5_3 sisyphus+325758.20.3.1 1690546231 installed
<13>Sep 2 01:59:51 rpmi: libqqwing-1.3.4-alt2 sisyphus+275255.100.2.1 1624562960 installed
<13>Sep 2 01:59:51 rpmi: qqwing-1.3.4-alt2 sisyphus+275255.100.2.1 1624562960 installed
<13>Sep 2 01:59:51 rpmi: libpotrace-1.16-alt2 sisyphus+328401.100.1.1 1693483624 installed
<13>Sep 2 01:59:51 rpmi: libpipeline-1.5.7-alt1_1 sisyphus+312433.100.1.1 1671879773 installed
<13>Sep 2 01:59:51 rpmi: man-db-2.11.2-alt1 sisyphus+324180.200.2.1 1688471215 installed
<13>Sep 2 01:59:52 rpmi: libpaper2-2:2.1.1-alt3 sisyphus+325767.100.2.2 1690582171 installed
<13>Sep 2 01:59:52 rpmi: liblcms2-2.15-alt1 sisyphus+316039.100.1.1 1677666328 installed
<13>Sep 2 01:59:52 rpmi: libxblas-1.0.248-alt2 sisyphus+285045.40.2.1 1631388330 installed
<13>Sep 2 01:59:52 rpmi: liblapack-1:3.8.0-alt7 sisyphus+293726.100.1.1 1642544497 installed
<13>Sep 2 01:59:52 rpmi: libkpathsea6-2021-alt5_3 sisyphus+325758.20.3.1 1690546231 installed
<13>Sep 2 01:59:52 rpmi: libptexenc1-2021-alt5_3 sisyphus+325758.20.3.1 1690546231 installed
<13>Sep 2 01:59:52 rpmi: libgomp1-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:52 rpmi: libgomp13-devel-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:52 rpmi: libnuma-2.0.14-alt2 sisyphus+278485.100.1.1 1626104244 installed
<13>Sep 2 01:59:52 rpmi: libx265-199-3.5-alt1.1 sisyphus+277560.100.1.1 1625697230 installed
<13>Sep 2 01:59:52 rpmi: librav1e-0.6.6-alt1 sisyphus+320651.100.1.1 1684313161 installed
<13>Sep 2 01:59:52 rpmi: desktop-file-utils-0.26-alt4 sisyphus+324226.100.1.1 1688469484 installed
<13>Sep 2 01:59:52 rpmi: shared-mime-info-2.2-alt1 sisyphus+297388.100.1.1 1648466615 installed
<13>Sep 2 01:59:52 rpmi: libgdk-pixbuf-locales-2.42.10-alt1 sisyphus+308991.100.1.1 1666721198 installed
<13>Sep 2 01:59:52 rpmi: libfribidi-1.0.13-alt1 sisyphus+320646.100.1.1 1684307082 installed
<13>Sep 2 01:59:52 rpmi: libde265-1.0.11-alt1 sisyphus+314940.100.1.1 1675940477 installed
<13>Sep 2 01:59:52 rpmi: libdav1d-1.2.1-alt1 sisyphus+323931.100.1.1 1688113641 installed
<13>Sep 2 01:59:52 rpmi: libdatrie-0.2.13-alt1_7 sisyphus+328221.100.1.1 1693336966 installed
<13>Sep 2 01:59:52 rpmi: libthai-0.1.29-alt1_6 sisyphus+328230.100.1.2 1693348044 installed
<13>Sep 2 01:59:52 rpmi: libaom3-3.5.0-alt1 sisyphus+312085.100.1.1 1671551546 installed
<13>Sep 2 01:59:52 rpmi: javazi-2023c-alt2 sisyphus+325007.200.2.1 1689531117 installed
<13>Sep 2 01:59:52 rpmi: hd2u-1.0.3-alt2 sisyphus+275312.100.2.1 1624906676 installed
<13>Sep 2 01:59:52 rpmi: gsettings-desktop-schemas-data-44.0-alt1 sisyphus+317076.300.1.1 1679344430 installed
<13>Sep 2 01:59:52 rpmi: libgio-2.76.5-alt1 sisyphus+328442.100.1.1 1693547696 installed
<13>Sep 2 01:59:52 rpmi: gsettings-desktop-schemas-44.0-alt1 sisyphus+317076.300.1.1 1679344430 installed
<13>Sep 2 01:59:52 rpmi: publicsuffix-list-dafsa-20230701-alt1 sisyphus+324303.100.1.1 1688561153 installed
<13>Sep 2 01:59:52 rpmi: libpsl-0.21.2-alt1 sisyphus+312536.100.1.1 1672131178 installed
<13>Sep 2 01:59:52 rpmi: libnghttp3.7-0.12.0-alt1 sisyphus+323677.20.3.1 1687690506 installed
<13>Sep 2 01:59:52 rpmi: libnghttp2-1.54.0-alt1 sisyphus+324359.10000.11.1 1689368798 installed
<13>Sep 2 01:59:52 rpmi: openldap-common-2.6.4-alt1 sisyphus+324359.600.5.1 1689262595 installed
<13>Sep 2 01:59:52 rpmi: libntlm-1.5-alt1 sisyphus+278100.3300.1.1 1626058899 installed
<13>Sep 2 01:59:52 rpmi: libidn-1.37-alt2 sisyphus+300849.100.1.1 1653769687 installed
<13>Sep 2 01:59:52 rpmi: libedit3-3.1.20221030-alt1 sisyphus+327935.100.1.1 1692980094 installed
<13>Sep 2 01:59:52 rpmi: libdeflate-1.18-alt1 sisyphus+317484.100.1.1 1679768609 installed
<13>Sep 2 01:59:52 rpmi: libtiff5-4.4.0-alt4 sisyphus+322581.100.1.2 1686180089 installed
<13>Sep 2 01:59:52 rpmi: libgdk-pixbuf-2.42.10-alt1 sisyphus+308991.100.1.1 1666721198 installed
<13>Sep 2 01:59:52 rpmi: libheif-1.15.2-alt1.1 sisyphus+328363.100.1.1 1693460604 installed
<13>Sep 2 01:59:52 rpmi: libpaper-1.1.28-alt4 sisyphus+325501.100.1.1 1690226535 installed
<13>Sep 2 01:59:52 rpmi: libopenjpeg2.0-2.5.0-alt1 sisyphus+299926.300.3.1 1652478843 installed
<13>Sep 2 01:59:52 rpmi: libverto-0.3.2-alt1_1 sisyphus+321176.2200.10.2 1684803947 installed
<13>Sep 2 01:59:52 rpmi: liblmdb-0.9.29-alt1.1 sisyphus+306630.100.1.1 1663072360 installed
<13>Sep 2 01:59:52 rpmi: libkeyutils-1.6.3-alt1 sisyphus+266061.100.1.1 1612919566 installed
<13>Sep 2 01:59:52 rpmi: libcom_err-1.46.4.0.5.4cda-alt1 sisyphus+283826.100.1.1 1629975345 installed
<13>Sep 2 01:59:52 rpmi: gcc-fortran-common-1.4.27-alt1 sisyphus+278099.1300.1.1 1626028636 installed
<13>Sep 2 01:59:52 rpmi: libgfortran13-devel-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:53 rpmi: gcc13-fortran-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:53 rpmi: gcc-c++-common-1.4.27-alt1 sisyphus+278099.1300.1.1 1626028636 installed
<13>Sep 2 01:59:53 rpmi: libstdc++13-devel-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:54 rpmi: gcc13-c++-13.2.1-alt2 sisyphus+327572.100.1.1 1692472816 installed
<13>Sep 2 01:59:54 rpmi: libX11-locales-3:1.8.6-alt1 sisyphus+323114.100.1.1 1686850054 installed
<13>Sep 2 01:59:54 rpmi: libXdmcp-1.1.4-alt1 sisyphus+311188.1000.1.1 1670233857 installed
<13>Sep 2 01:59:54 rpmi: libxcb-1.16-alt1 sisyphus+327325.200.1.1 1692276261 installed
<13>Sep 2 01:59:54 rpmi: libX11-3:1.8.6-alt1 sisyphus+323114.100.1.1 1686850054 installed
<13>Sep 2 01:59:54 rpmi: libXext-1.3.5-alt1 sisyphus+309285.100.1.1 1667212412 installed
<13>Sep 2 01:59:54 rpmi: libXt-1.2.1-alt1 sisyphus+265202.200.1.1 1611565457 installed
<13>Sep 2 01:59:54 rpmi: libXmu-1.1.4-alt1 sisyphus+308663.1000.1.1 1666168409 installed
<13>Sep 2 01:59:54 rpmi: libXrender-0.9.11-alt1 sisyphus+308841.100.1.1 1666436130 installed
<13>Sep 2 01:59:54 rpmi: libcairo-1:1.17.8-alt1 sisyphus+324101.100.2.1 1690287710 installed
<13>Sep 2 01:59:54 rpmi: libXft-2.3.7-alt1 sisyphus+310164.100.1.1 1668680608 installed
<13>Sep 2 01:59:54 rpmi: libXpm-3.5.15-alt1 sisyphus+313628.100.1.1 1674030938 installed
<13>Sep 2 01:59:55 rpmi: libxcb-devel-1.16-alt1 sisyphus+327325.200.1.1 1692276261 installed
<13>Sep 2 01:59:55 rpmi: libX11-devel-3:1.8.6-alt1 sisyphus+323114.100.1.1 1686850054 installed
<13>Sep 2 01:59:55 rpmi: libXrender-devel-0.9.11-alt1 sisyphus+308841.100.1.1 1666436130 installed
<13>Sep 2 01:59:55 rpmi: libXext-devel-1.3.5-alt1 sisyphus+309285.100.1.1 1667212412 installed
<13>Sep 2 01:59:55 rpmi: libXt-devel-1.2.1-alt1 sisyphus+265202.200.1.1 1611565457 installed
<13>Sep 2 01:59:55 rpmi: libXaw-1.0.14-alt1 sisyphus+284644.100.1.1 1630910247 installed
<13>Sep 2 01:59:55 rpmi: libgd3-2.3.3-alt1 sisyphus+286379.100.1.1 1633353307 installed
<13>Sep 2 01:59:55 rpmi: libpango-1.50.14-alt1 sisyphus+316117.100.1.1 1677780551 installed
<13>Sep 2 01:59:55 rpmi: libtk-8.6.13-alt1 sisyphus+310696.200.1.1 1669548530 installed
<13>Sep 2 01:59:55 rpmi: tk-8.6.13-alt1 sisyphus+310696.200.1.1 1669548530 installed
<13>Sep 2 01:59:55 rpmi: perl-Tk-804.036-alt1 sisyphus+279723.3300.1.1 1626649879 installed
<13>Sep 2 01:59:55 rpmi: libharfbuzz-cairo-8.1.1-alt1 sisyphus+326343.100.1.1 1691060130 installed
<13>Sep 2 01:59:55 rpmi: xset-1.2.4-alt1 sisyphus+275497.100.2.2 1624918317 installed
<13>Sep 2 01:59:55 rpmi: xprop-1.2.5-alt1 sisyphus+279025.100.1.1 1626354198 installed
<13>Sep 2 01:59:55 rpmi: xdg-utils-1.1.3-alt12 sisyphus+303279.300.3.1 1657254392 installed
<13>Sep 2 01:59:55 rpmi: libmpdec3-2.5.1-alt3 sisyphus+314490.500.5.1 1675432004 installed
<13>Sep 2 01:59:55 rpmi: libb2-0.98.1-alt1_1 sisyphus+291614.100.1.1 1638962877 installed
<13>Sep 2 01:59:55 rpmi: ed-1:0.2-alt10 sisyphus+278100.1100.1.1 1626056843 installed
<13>Sep 2 01:59:55 rpmi: diffstat-1.64-alt1 sisyphus+278100.700.1.1 1626056683 installed
<13>Sep 2 01:59:55 rpmi: libdialog-1.3.20171209-alt2 sisyphus+328094.100.1.1 1693228848 installed
<13>Sep 2 01:59:55 rpmi: dialog-1.3.20171209-alt2 sisyphus+328094.100.1.1 1693228848 installed
<13>Sep 2 01:59:55 rpmi: bc-1:1.07.1-alt1 sisyphus+278100.400.1.1 1626056612 installed
<13>Sep 2 01:59:55 rpmi: rpm-macros-alternatives-0.5.2-alt2 sisyphus+315270.200.2.1 1676457367 installed
<13>Sep 2 01:59:55 rpmi: alternatives-0.5.2-alt2 sisyphus+315270.200.2.1 1676457367 installed
<13>Sep 2 01:59:55 rpmi: ca-certificates-2023.07.31-alt1 sisyphus+326137.200.1.1 1690809798 installed
<13>Sep 2 01:59:55 rpmi: ca-trust-0.1.4-alt1 sisyphus+308690.100.1.1 1666182992 installed
<13>Sep 2 01:59:55 rpmi: p11-kit-trust-1:0.24.1-alt2 sisyphus+324666.100.1.1 1689083439 installed
<13>Sep 2 01:59:55 rpmi: libcrypto3-3.1.2-alt1 sisyphus+326244.100.1.1 1690906741 installed
<13>Sep 2 01:59:55 rpmi: libssl3-3.1.2-alt1 sisyphus+326244.100.1.1 1690906741 installed
<86>Sep 2 01:59:55 groupadd[3261660]: group added to /etc/group: name=_keytab, GID=999
<86>Sep 2 01:59:55 groupadd[3261660]: group added to /etc/gshadow: name=_keytab
<86>Sep 2 01:59:55 groupadd[3261660]: new group: name=_keytab, GID=999
<13>Sep 2 01:59:55 rpmi: libkrb5-1.21.2-alt1 sisyphus+327265.100.1.1 1692185462 installed
<13>Sep 2 01:59:55 rpmi: python3-3.11.4-alt2 sisyphus+324359.500.4.1 1689257961 installed
<13>Sep 2 01:59:56 rpmi: python3-base-3.11.4-alt2 sisyphus+324359.500.4.1 1689257961 installed
<13>Sep 2 01:59:56 rpmi: glib2-devel-2.76.5-alt1 sisyphus+328442.100.1.1 1693547696 installed
<13>Sep 2 01:59:56 rpmi: libcairo-devel-1:1.17.8-alt1 sisyphus+324101.100.2.1 1690287710 installed
<13>Sep 2 01:59:56 rpmi: fontconfig-devel-2.14.2-alt8 sisyphus+328444.100.1.1 1693553402 installed
<13>Sep 2 01:59:56 rpmi: libfreetype-devel-2.13.1-alt1 sisyphus+324353.100.1.1 1688638057 installed
<13>Sep 2 01:59:56 rpmi: libharfbuzz-devel-8.1.1-alt1 sisyphus+326343.100.1.1 1691060130 installed
<13>Sep 2 01:59:56 rpmi: libXft-devel-2.3.7-alt1 sisyphus+310164.100.1.1 1668680608 installed
<13>Sep 2 01:59:56 rpmi: libcups-2.4.2-alt3 sisyphus+325006.300.1.1 1689495737 installed
<13>Sep 2 01:59:57 rpmi: libgs-10.01.1-alt1 sisyphus+318450.100.1.1 1681389065 installed
<13>Sep 2 01:59:57 rpmi: ghostscript-common-10.01.1-alt1 sisyphus+318450.100.1.1 1681389065 installed
<13>Sep 2 01:59:57 rpmi: ghostscript-classic-10.01.1-alt1 sisyphus+318450.100.1.1 1681389065 installed
<13>Sep 2 01:59:58 rpmi: ghostscript-10.01.1-alt1 sisyphus+318450.100.1.1 1681389065 installed
<13>Sep 2 01:59:58 rpmi: ghostscript-module-X-10.01.1-alt1 sisyphus+318450.100.1.1 1681389065 installed
<13>Sep 2 01:59:58 rpmi: libgsasl-1.8.0-alt3 sisyphus+275307.100.1.2 1624478543 installed
<86>Sep 2 01:59:58 groupadd[3263844]: group added to /etc/group: name=sasl, GID=998
<86>Sep 2 01:59:58 groupadd[3263844]: group added to /etc/gshadow: name=sasl
<86>Sep 2 01:59:58 groupadd[3263844]: new group: name=sasl, GID=998
<13>Sep 2 01:59:58 rpmi: libsasl2-3-2.1.27-alt2.2 sisyphus+324359.6000.12.1 1689392001 installed
<13>Sep 2 01:59:58 rpmi: libldap2-2.6.4-alt1 sisyphus+324359.600.5.1 1689262595 installed
<13>Sep 2 01:59:58 rpmi: perl-Net-SSLeay-1.92-alt1 sisyphus+325072.500.5.1 1689613736 installed
<13>Sep 2 01:59:58 rpmi: perl-IO-Socket-SSL-2.083-alt1 sisyphus+321544.100.1.2 1684665884 installed
<13>Sep 2 01:59:58 rpmi: perl-Net-HTTPS-6.23-alt1 sisyphus+323470.100.1.1 1687422469 installed
<13>Sep 2 01:59:58 rpmi: perl-LWP-Protocol-https-6.11-alt1 sisyphus+325810.100.1.2 1690571190 installed
<13>Sep 2 01:59:58 rpmi: openssh-common-9.4p1-alt1 sisyphus+327935.1700.3.1 1692995983 installed
<86>Sep 2 01:59:58 groupadd[3263864]: group added to /etc/group: name=sshagent, GID=997
<86>Sep 2 01:59:58 groupadd[3263864]: group added to /etc/gshadow: name=sshagent
<86>Sep 2 01:59:58 groupadd[3263864]: new group: name=sshagent, GID=997
<13>Sep 2 01:59:58 rpmi: openssh-clients-9.4p1-alt1 sisyphus+327935.1700.3.1 1692995983 installed
<13>Sep 2 01:59:58 rpmi: rsync-3.2.7-alt1 sisyphus+325006.2000.1.1 1689497333 installed
<13>Sep 2 01:59:58 rpmi: libssh2-1.11.0-alt1 sisyphus+327652.100.1.1 1692636577 installed
<13>Sep 2 01:59:58 rpmi: libcurl-8.2.1-alt1 sisyphus+326951.100.1.1 1691770183 installed
<13>Sep 2 01:59:58 rpmi: git-core-2.33.8-alt1 sisyphus+324359.6600.12.1 1689393343 installed
<13>Sep 2 01:59:58 rpmi: ca-trust-java-0.1.4-alt1 sisyphus+308690.100.1.1 1666182992 installed
<13>Sep 2 01:59:58 rpmi: foomatic-db-engine-4.0.12-alt1 sisyphus+278189.100.1.1 1626076171 installed
<13>Sep 2 01:59:59 rpmi: texlive-2021-alt5_3 sisyphus+325758.20.3.1 1690546231 installed
<13>Sep 2 02:00:07 rpmi: texlive-collection-basic-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed
<13>Sep 2 02:00:09 rpmi: texlive-fonts-sources-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed
<13>Sep 2 02:00:09 rpmi: texlive-texmf-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed
<13>Sep 2 02:00:43 rpmi: texlive-dist-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed
<13>Sep 2 02:00:43 rpmi: alsa-ucm-conf-1.2.8-alt8 sisyphus+322508.200.2.1 1687380386 installed
<13>Sep 2 02:00:43 rpmi: alsa-topology-conf-1.2.5.1-alt1 sisyphus+274777.100.1.1 1624089141 installed
<13>Sep 2 02:00:43 rpmi: libalsa-1:1.2.8-alt1 sisyphus+310349.200.1.1 1668964316 installed
<13>Sep 2 02:00:45 rpmi: java-17-openjdk-headless-0:17.0.8.0.7-alt1 sisyphus+327853.100.2.3 1692923582 installed
<13>Sep 2 02:00:46 rpmi: libcurl-devel-8.2.1-alt1 sisyphus+326951.100.1.1 1691770183 installed
<13>Sep 2 02:00:46 rpmi: libpango-devel-1.50.14-alt1 sisyphus+316117.100.1.1 1677780551 installed
<13>Sep 2 02:00:46 rpmi: tk-devel-8.6.13-alt1 sisyphus+310696.200.1.1 1669548530 installed
<13>Sep 2 02:00:46 rpmi: libXmu-devel-1.1.4-alt1 sisyphus+308663.1000.1.1 1666168409 installed
<13>Sep 2 02:00:46 rpmi: gcc-c++-13-alt1 sisyphus+323337.300.1.1 1687267966 installed
<13>Sep 2 02:00:46 rpmi: gcc-fortran-13-alt1 sisyphus+323337.300.1.1 1687267966 installed
<13>Sep 2 02:00:46 rpmi: libtiff-devel-4.4.0-alt4 sisyphus+322581.100.1.2 1686180089 installed
<13>Sep 2 02:00:46 rpmi: libgomp-devel-13-alt1 sisyphus+323337.300.1.1 1687267966 installed
<13>Sep 2 02:00:46 rpmi: liblapack-devel-1:3.8.0-alt7 sisyphus+293726.100.1.1 1642544497 installed
<13>Sep 2 02:00:46 rpmi: libtre-devel-0.8.0-alt2.2 sisyphus+278356.100.1.1 1626091408 installed
<13>Sep 2 02:00:46 rpmi: makeinfo-6.7-alt1 sisyphus+328181.1400.3.1 1693325447 installed
<13>Sep 2 02:00:46 rpmi: texi2dvi-6.7-alt1 sisyphus+328181.1400.3.1 1693325447 installed
<13>Sep 2 02:00:46 rpmi: libjpeg-devel-2:2.1.2-alt1.2 sisyphus+300827.100.2.1 1653916633 installed
<13>Sep 2 02:00:46 rpmi: libreadline-devel-7.0.3-alt4 sisyphus+328124.200.1.1 1693248140 installed
<13>Sep 2 02:00:46 rpmi: libpcre2-devel-10.42-alt1 sisyphus+311927.100.1.1 1671290951 installed
<13>Sep 2 02:00:46 rpmi: liblzma-devel-5.2.5-alt3.1 sisyphus+291400.100.1.1 1638634809 installed
<13>Sep 2 02:00:46 rpmi: bzlib-devel-1:1.0.8-alt2 sisyphus+283723.100.1.1 1629847653 installed
egrep: warning: egrep is obsolescent; using grep -E
Building target platforms: x86_64
Building for target x86_64
Wrote: /usr/src/in/nosrpm/R-base-4.2.2-alt1.nosrc.rpm (w1.gzdio)
Installing R-base-4.2.2-alt1.src.rpm
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.47253
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ rm -rf R-4.2.2
+ echo 'Source #0 (R-4.2.2.tar):'
Source #0 (R-4.2.2.tar):
+ /bin/tar -xf /usr/src/RPM/SOURCES/R-4.2.2.tar
+ cd R-4.2.2
+ /bin/chmod -c -Rf u+rwX,go-w .
+ echo 'Patch #0 (R-4.2.2-alt1.patch):'
Patch #0 (R-4.2.2-alt1.patch):
+ /usr/bin/patch -p1
patching file .gear/R-base-4.1.3-alt-fix-build-libcurl8.patch
patching file .gear/rules
patching file .gear/tags/090724dbb6a4b610aebe571d65fd3f728697d791
patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0
patching file .gear/tags/1af743c7e25d963067c0a7736c2f362bc1a54087
patching file .gear/tags/1c120fe0028c5f64c67f1a04eeed89140e84044a
patching file .gear/tags/2c68f436cffd98cb9581510d928bea5942555c48
patching file .gear/tags/54c0af5d3e579ef9d459def6e87471043832c3ed
patching file .gear/tags/70ae5201e8ecc68e51ed59c0bedcfa01dbb4b579
patching file .gear/tags/890191223501f9206c89761358c534357f6c76b8
patching file .gear/tags/927c0ab3556c90b625751594da83a9926a6014d6
patching file .gear/tags/9bcb4bdb4dd1185d3f43ac2d1ba0d8a70921a4e0
patching file .gear/tags/a267957eb382565da32225335ac89fb8c75df0da
patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5
patching file .gear/tags/a8802667f7d1597d2cd5442d00d4d4773505446e
patching file .gear/tags/b058f2b5de79631ea567c44d0a2ef87939a28ec5
patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020
patching file .gear/tags/d1aa04cfbb52bb55a5c03a5323d797c2bf87b6a9
patching file .gear/tags/d4cbf2db4bf99fe20d6f904178cbebb8619dab9a
patching file .gear/tags/dbe24e8137437d3688e1d77cf1b67279d3099cea
patching file .gear/tags/e6f3c8b737583c5e27038507647866d029bfb5e4
patching file .gear/tags/ebdb5ee7ba9a5499c21aadcfee3318a7d6d52061
patching file .gear/tags/eca5e30f29900b6f8279889e83a532a8cb55697a
patching file .gear/tags/eef29626bf3bf68c9462ce5f0594fedd5a80168b
patching file .gear/tags/f1447dd74acee19fdf9c5adc838da57bef3c8142
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 tests/d-p-q-r-tst-2.R
patching file tests/reg-tests-1c.R
patching file tests/reg-tests-1d.R
+ echo 'Patch #1 (R-base-4.1.3-alt-fix-build-libcurl8.patch):'
Patch #1 (R-base-4.1.3-alt-fix-build-libcurl8.patch):
+ /usr/bin/patch -p1
patching file configure
Hunk #1 succeeded at 47584 (offset 156 lines).
Hunk #2 succeeded at 47602 (offset 156 lines).
patching file m4/R.m4
Hunk #1 succeeded at 4300 (offset 29 lines).
+ 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.47253
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-4.2.2
+ 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=xdg-open ac_cv_path_R_PDFVIEWER=xdg-open '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=xdg-open
+ ac_cv_path_R_PDFVIEWER=xdg-open
+ ac_cv_path_PAGER='less -isR'
+ ac_cv_prog_R_PRINTCMD=lpr
+ CFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing'
+ export CFLAGS
+ CXXFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing'
+ export CXXFLAGS
+ FFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing'
+ export FFLAGS
+ FCFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing'
+ export FCFLAGS
+ '[' -n '' ']'
++ printf %s '-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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
+ readlink -e -- ./configure
+ xargs -ri dirname -- '{}'
+ xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n'
+ sort -u
+ xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess
+ configure_runstatedir_flags=
+ grep -qF runstatedir=DIR ./configure
+ configure_runstatedir_flags=--runstatedir=/var/run
+ ./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 --disable-silent-rules --runstatedir=/var/run --without-included-gettext --enable-prebuilt-html --enable-R-shlib --with-x --disable-rpath --with-system-tre --with-gnu-ld --enable-long-double --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-4.2'
configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules
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 whether ln -s works... yes
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) xdg-open
using default browser ... xdg-open
checking for acroread... (cached) xdg-open
checking for working aclocal... found
checking for working autoconf... found
checking for working autoheader... found
checking for bison... bison -y
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 the compiler supports GNU C... yes
checking whether x86_64-alt-linux-gcc accepts -g... yes
checking for x86_64-alt-linux-gcc option to enable C11 features... 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 stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for wchar.h... yes
checking for minix/config.h... no
checking for sys/time.h... yes
checking for sys/param.h... yes
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
looking for a modern Fortran compiler
checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran
checking whether the compiler supports GNU Fortran... yes
checking whether x86_64-alt-linux-gfortran accepts -g... yes
checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++
checking whether the compiler supports GNU C++... yes
checking whether x86_64-alt-linux-g++ accepts -g... yes
checking for x86_64-alt-linux-g++ option to enable C++11 features... none needed
checking whether x86_64-alt-linux-g++ -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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 x86_64-alt-linux-g++ accepts -fvisibility... yes
checking whether x86_64-alt-linux-gfortran accepts -fvisibility... yes
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether the compiler supports GNU Objective C... no
checking whether x86_64-alt-linux-gcc accepts -g... no
checking whether x86_64-alt-linux-g++ can compile ObjC++... no
checking for Objective C++ compiler... 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 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 cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking for readline/history.h... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking for tilde_expand_word... yes
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 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 for fcntl.h... yes
checking for glob.h... yes
checking for grp.h... yes
checking for pwd.h... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking for sys/resource.h... yes
checking for sys/select.h... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/time.h... (cached) yes
checking for sys/times.h... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking for utime.h... yes
checking for arpa/inet.h... yes
checking for elf.h... yes
checking for features.h... yes
checking for floatingpoint.h... no
checking for langinfo.h... yes
checking for netdb.h... yes
checking for netinet/in.h... yes
checking for sys/param.h... (cached) yes
checking for stdalign.h... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... yes
checking for locale.h... yes
checking for stdarg.h... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking for x86_64-alt-linux-gcc options needed to detect all undeclared functions... none needed
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 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 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 for C stack direction... down
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... -fopenmp
checking how to get verbose linking output from x86_64-alt-linux-gfortran... -v
checking for Fortran libraries of x86_64-alt-linux-gfortran... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/13 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../.. -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/13 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../.. -lgcc_s
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether x86_64-alt-linux-gfortran appends underscores to external names... yes
checking whether x86_64-alt-linux-gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on int and double... yes
checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on double complex... yes
checking for x86_64-alt-linux-gfortran option to support OpenMP... -fopenmp
checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes
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 if need -fno-optimize-sibling-calls for gfortran... yes
checking for type of 'hidden' Fortran character lengths... size_t
checking for xmkmf... 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 with -std=gnu++14... yes
checking whether x86_64-alt-linux-g++ supports C++17 features with -std=gnu++17... yes
checking whether x86_64-alt-linux-g++ supports C++20 features with -std=gnu++20... yes
checking for x86_64-alt-linux-g++ -std=gnu++14 option to support OpenMP... -fopenmp
checking for option providing pthread_kill... none required
checking whether POSIX threads are supported... yes
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 rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
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... no
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwnam 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 setrlimit 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 thread.h... no
checking whether thr_stksegment exists and is declared... no
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... no
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 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 for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking whether iconv accepts "CP1252"... 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 for wchar.h... (cached) 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 wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking whether wcwidth exists and is declared... yes
checking whether wcswidth 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 for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... 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 for tcl.h... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking for rpc/types.h... no
checking for tirpc/rpc/types.h... no
checking for XDR support... no
checking for inflateInit2_ in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking for BZ2_bzlibVersion in -lbz2... 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 for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre2.h... yes
checking for pcre2_compile_8 in -lpcre2-8... yes
checking if PCRE2 has Unicode support... 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 ... 8.2.1
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.28.0 or 8... yes
checking if libcurl supports https... yes
checking if pkg-config knows about libjpeg... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if pkg-config knows about libpng... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking if pkg-config knows about libtiff... 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 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... false
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... (cached) -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
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checking for simple visibility declarations... yes
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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
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extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
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checking for bison... bison
checking version of bison... 3.7.6, ok
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checking whether _snprintf is declared... no
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checking for CFPreferencesCopyAppValue... (cached) no
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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... yes
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
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configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules
R is now configured for x86_64-alt-linux-gnu
Source directory: .
Installation directory: /usr
C compiler: x86_64-alt-linux-gcc -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
Fortran fixed-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
Default C++ compiler: x86_64-alt-linux-g++ -std=gnu++14 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
C++11 compiler: x86_64-alt-linux-g++ -std=gnu++11 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
C++14 compiler: x86_64-alt-linux-g++ -std=gnu++14 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
C++17 compiler: x86_64-alt-linux-g++ -std=gnu++17 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
C++20 compiler: x86_64-alt-linux-g++ -std=gnu++20 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
Fortran free-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing
Obj-C compiler: x86_64-alt-linux-gcc
Interfaces supported: X11, tcltk
External libraries: pcre2, 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
+ make -j16
make[1]: Nothing to be done for 'R'.
make[1]: Nothing to be done for 'R'.
make[2]: Nothing to be done for 'R'.
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts'
creating src/scripts/R.fe
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/include'
mkdir -p -- ../../include
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mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/include/R_ext'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
making xdr_float.d from xdr_float.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
making xdr.d from xdr.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
making xdr_stdio.d from xdr_stdio.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
making xdr_mem.d from xdr_mem.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making regcomp.d from regcomp.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making regerror.d from regerror.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-ast.d from tre-ast.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-mem.d from tre-mem.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-match-approx.d from tre-match-approx.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-match-parallel.d from tre-match-parallel.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-compile.d from tre-compile.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-match-backtrack.d from tre-match-backtrack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making regexec.d from regexec.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-stack.d from tre-stack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making xmalloc.d from xmalloc.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
making tre-parse.d from tre-parse.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr_float.c -o xdr_float.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr_mem.c -o xdr_mem.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr.c -o xdr.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr_stdio.c -o xdr_stdio.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
ar -cr libxdr.a xdr.o xdr_float.o xdr_mem.o xdr_stdio.o
ranlib libxdr.a
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o
xmalloc.c: In function 'xrealloc_impl':
xmalloc.c:358:7: warning: pointer 'ptr_19(D)' may be used after 'realloc' [-Wuse-after-free]
358 | hash_table_del(xmalloc_table, ptr);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xmalloc.c:355:13: note: call to 'realloc' here
355 | new_ptr = realloc(ptr, new_size);
| ^~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre'
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-4.2.2/src/extra/tre'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
making interv.d from interv.c
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making integrate.d from integrate.c
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making maxcol.d from maxcol.c
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making pretty.d from pretty.c
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making optim.d from optim.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
making uncmin.d from uncmin.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpbfa.f -o dpbfa.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpbsl.f -o dpbsl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpoco.f -o dpoco.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpodi.f -o dpodi.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c interv.c -o interv.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpofa.f -o dpofa.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dchdc.f -o dchdc.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dposl.f -o dposl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c maxcol.c -o maxcol.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrdc.f -o dqrdc.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pretty.c -o pretty.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrls.f -o dqrls.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtrsl.f -o dtrsl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrutl.f -o dqrutl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrsl.f -o dqrsl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtrco.f -o dtrco.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c integrate.c -o integrate.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dsvdc.f -o dsvdc.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c uncmin.c -o uncmin.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c optim.c -o optim.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
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-4.2.2/src/appl'
#@make install-Linpack
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making mlutils.d from mlutils.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making fmax2.d from fmax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making ftrunc.d from ftrunc.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making fround.d from fround.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making i1mach.d from i1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making d1mach.d from d1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making fmin2.d from fmin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making sign.d from sign.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making fsign.d from fsign.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making imax2.d from imax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making imin2.d from imin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making chebyshev.d from chebyshev.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making fprec.d from fprec.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making gammalims.d from gammalims.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making log1p.d from log1p.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making lgammacor.d from lgammacor.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making stirlerr.d from stirlerr.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making bd0.d from bd0.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making gamma.d from gamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making lgamma.d from lgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making gamma_cody.d from gamma_cody.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making beta.d from beta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making lbeta.d from lbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making polygamma.d from polygamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making bessel_i.d from bessel_i.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making bessel_j.d from bessel_j.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making cospi.d from cospi.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making bessel_k.d from bessel_k.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making bessel_y.d from bessel_y.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making choose.d from choose.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making snorm.d from snorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making sexp.d from sexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dgamma.d from dgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making pgamma.d from pgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making qgamma.d from qgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making rgamma.d from rgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dbeta.d from dbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making rbeta.d from rbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making pbeta.d from pbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making qbeta.d from qbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dunif.d from dunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making punif.d from punif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making runif.d from runif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making qunif.d from qunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dnorm.d from dnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making pnorm.d from pnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making qnorm.d from qnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dlnorm.d from dlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making plnorm.d from plnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making rnorm.d from rnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making rlnorm.d from rlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making qlnorm.d from qlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making df.d from df.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making pf.d from pf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making qf.d from qf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making rf.d from rf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dnf.d from dnf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dt.d from dt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making pt.d from pt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making qt.d from qt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making rt.d from rt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dnt.d from dnt.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making pchisq.d from pchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
making dchisq.d from dchisq.c
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making qchisq.d from qchisq.c
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making rnchisq.d from rnchisq.c
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making rchisq.d from rchisq.c
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making dbinom.d from dbinom.c
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making pbinom.d from pbinom.c
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making qbinom.d from qbinom.c
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making dcauchy.d from dcauchy.c
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making rbinom.d from rbinom.c
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making rmultinom.d from rmultinom.c
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making pcauchy.d from pcauchy.c
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making qcauchy.d from qcauchy.c
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making rcauchy.d from rcauchy.c
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making pexp.d from pexp.c
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making dexp.d from dexp.c
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making rexp.d from rexp.c
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making dgeom.d from dgeom.c
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making pgeom.d from pgeom.c
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making qexp.d from qexp.c
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making qgeom.d from qgeom.c
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making rgeom.d from rgeom.c
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making phyper.d from phyper.c
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making dhyper.d from dhyper.c
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making qhyper.d from qhyper.c
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making dnbinom.d from dnbinom.c
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making rhyper.d from rhyper.c
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making pnbinom.d from pnbinom.c
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making qnbinom.d from qnbinom.c
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making qnbinom_mu.d from qnbinom_mu.c
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making rnbinom.d from rnbinom.c
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making ppois.d from ppois.c
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making dpois.d from dpois.c
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making qpois.d from qpois.c
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making rpois.d from rpois.c
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making dweibull.d from dweibull.c
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making pweibull.d from pweibull.c
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making qweibull.d from qweibull.c
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making rweibull.d from rweibull.c
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making dlogis.d from dlogis.c
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making plogis.d from plogis.c
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making qlogis.d from qlogis.c
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making rlogis.d from rlogis.c
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making dnchisq.d from dnchisq.c
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making pnchisq.d from pnchisq.c
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making qnchisq.d from qnchisq.c
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making dnbeta.d from dnbeta.c
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making pnbeta.d from pnbeta.c
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making qnbeta.d from qnbeta.c
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making pnf.d from pnf.c
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making qnt.d from qnt.c
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making qnf.d from qnf.c
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making signrank.d from signrank.c
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making qtukey.d from qtukey.c
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making pnt.d from pnt.c
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making ptukey.d from ptukey.c
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making wilcox.d from wilcox.c
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making toms708.d from toms708.c
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c d1mach.c -o d1mach.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fmin2.c -o fmin2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fmax2.c -o fmax2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ftrunc.c -o ftrunc.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sign.c -o sign.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fsign.c -o fsign.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c i1mach.c -o i1mach.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fround.c -o fround.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c imax2.c -o imax2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c imin2.c -o imin2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fprec.c -o fprec.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mlutils.c -o mlutils.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chebyshev.c -o chebyshev.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c log1p.c -o log1p.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lgammacor.c -o lgammacor.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gammalims.c -o gammalims.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stirlerr.c -o stirlerr.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lgamma.c -o lgamma.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gamma.c -o gamma.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c beta.c -o beta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bd0.c -o bd0.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lbeta.c -o lbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cospi.c -o cospi.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rcauchy.c -o rcauchy.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dexp.c -o dexp.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rexp.c -o rexp.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qexp.c -o qexp.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pexp.c -o pexp.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgeom.c -o dgeom.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dhyper.c -o dhyper.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rgeom.c -o rgeom.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pgeom.c -o pgeom.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qgeom.c -o qgeom.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnbinom.c -o pnbinom.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qhyper.c -o qhyper.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnbinom.c -o qnbinom.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnbinom_mu.c -o qnbinom_mu.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c phyper.c -o phyper.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnbinom.c -o dnbinom.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpois.c -o dpois.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qpois.c -o qpois.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pweibull.c -o pweibull.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qweibull.c -o qweibull.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dlogis.c -o dlogis.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qlogis.c -o qlogis.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rlogis.c -o rlogis.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnchisq.c -o dnchisq.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnf.c -o pnf.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnchisq.c -o pnchisq.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qtukey.c -o qtukey.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnchisq.c -o qnchisq.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnbeta.c -o pnbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnbeta.c -o dnbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnbeta.c -o qnbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnf.c -o qnf.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnt.c -o pnt.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnt.c -o qnt.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c wilcox.c -o wilcox.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c signrank.c -o signrank.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ptukey.c -o ptukey.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c toms708.c -o toms708.o
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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 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 qnbinom_mu.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
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making dynload.d from dynload.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
making system.d from system.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c X11.c -o X11.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dynload.c -o dynload.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rembedded.c -o Rembedded.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c system.c -o system.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sys-unix.c -o sys-unix.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sys-std.c -o sys-std.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
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-4.2.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-4.2.2"' \
-o Rscript ./Rscript.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
config.status: creating src/main/Makefile
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making CommandLineArgs.d from CommandLineArgs.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making Rdynload.d from Rdynload.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making Renviron.d from Renviron.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making RNG.d from RNG.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making altrep.d from altrep.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making agrep.d from agrep.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making apply.d from apply.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making attrib.d from attrib.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making bind.d from bind.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making altclasses.d from altclasses.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making arithmetic.d from arithmetic.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making array.d from array.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making builtin.d from builtin.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making character.d from character.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making clippath.d from clippath.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making colors.d from colors.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making complex.d from complex.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making coerce.d from coerce.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making cum.d from cum.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making context.d from context.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making datetime.d from datetime.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making dcf.d from dcf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making debug.d from debug.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making deparse.d from deparse.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making connections.d from connections.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making devices.d from devices.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making dstruct.d from dstruct.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making duplicate.d from duplicate.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making dotcode.d from dotcode.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making dounzip.d from dounzip.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making edit.d from edit.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making engine.d from engine.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making envir.d from envir.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making gevents.d from gevents.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making format.d from format.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making gram-ex.d from gram-ex.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making errors.d from errors.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making eval.d from eval.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making gram.d from gram.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making graphics.d from graphics.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making identical.d from identical.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making inlined.d from inlined.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making grep.d from grep.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making inspect.d from inspect.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
making localecharset.d from localecharset.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making internet.d from internet.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making iosupport.d from iosupport.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making lapack.d from lapack.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making list.d from list.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making logic.d from logic.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making main.d from main.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making mapply.d from mapply.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making mask.d from mask.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making match.d from match.c
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making memory.d from memory.c
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making names.d from names.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making options.d from options.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making paste.d from paste.c
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making patterns.d from patterns.c
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making objects.d from objects.c
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making plot.d from plot.c
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making plotmath.d from plotmath.c
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making plot3d.d from plot3d.c
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making print.d from print.c
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making printarray.d from printarray.c
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making platform.d from platform.c
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making printvector.d from printvector.c
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making qsort.d from qsort.c
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making random.d from random.c
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making raw.d from raw.c
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making registration.d from registration.c
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making printutils.d from printutils.c
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making radixsort.d from radixsort.c
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making relop.d from relop.c
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making rlocale.d from rlocale.c
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making saveload.d from saveload.c
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making seq.d from seq.c
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making sort.d from sort.c
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making scan.d from scan.c
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making source.d from source.c
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making serialize.d from serialize.c
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making split.d from split.c
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making sprintf.d from sprintf.c
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making subassign.d from subassign.c
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making subscript.d from subscript.c
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making startup.d from startup.c
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making subset.d from subset.c
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making summary.d from summary.c
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making g_alab_her.d from g_alab_her.c
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making times.d from times.c
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making unique.d from unique.c
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making alloca.d from alloca.c
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making sysutils.d from sysutils.c
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making Rmain.d from Rmain.c
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making strncasecmp.d from strncasecmp.c
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making version.d from version.c
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making strdup.d from strdup.c
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making g_fontdb.d from g_fontdb.c
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making g_cntrlify.d from g_cntrlify.c
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making mkdtemp.d from mkdtemp.c
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making util.d from util.c
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making g_her_glyph.d from g_her_glyph.c
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Renviron.c -o Renviron.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c RNG.c -o RNG.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c apply.c -o apply.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c altrep.c -o altrep.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rdynload.c -o Rdynload.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clippath.c -o clippath.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agrep.c -o agrep.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c altclasses.c -o altclasses.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bind.c -o bind.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c colors.c -o colors.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c attrib.c -o attrib.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cum.c -o cum.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c builtin.c -o builtin.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c complex.c -o complex.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c context.c -o context.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c debug.c -o debug.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dcf.c -o dcf.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c character.c -o character.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c array.c -o array.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devices.c -o devices.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dstruct.c -o dstruct.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coerce.c -o coerce.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c edit.c -o edit.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c deparse.c -o deparse.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dounzip.c -o dounzip.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c datetime.c -o datetime.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c duplicate.c -o duplicate.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c arithmetic.c -o arithmetic.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gevents.c -o gevents.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gram-ex.c -o gram-ex.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c format.c -o format.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c graphics.c -o graphics.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c iosupport.c -o iosupport.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c identical.c -o identical.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c inspect.c -o inspect.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c localecharset.c -o localecharset.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c engine.c -o engine.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c inlined.c -o inlined.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c internet.c -o internet.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lapack.c -o lapack.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c list.c -o list.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dotcode.c -o dotcode.o
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c connections.c -o connections.o
connections.c: In function 'do_readLines':
connections.c:4008:21: warning: pointer 'buf_89' may be used after 'realloc' [-Wuse-after-free]
4008 | free(buf);
| ^~~~~~~~~
connections.c:4006:38: note: call to 'realloc' here
4006 | char *tmp = (char *) realloc(buf, buf_size);
| ^~~~~~~~~~~~~~~~~~~~~~
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c summary.c -o summary.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sysutils.c -o sysutils.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c subset.c -o subset.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sort.c -o sort.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c subassign.c -o subassign.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c util.c -o util.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c eval.c -o eval.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c unique.c -o unique.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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x86_64-alt-linux-gcc -shared -fopenmp -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o clippath.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 mask.o match.o memory.o names.o objects.o options.o paste.o patterns.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 ../extra/xdr/libxdr.a -lopenblas -lgfortran -lm -lquadmath -lreadline -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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mkdir -p -- /usr/src/RPM/BUILD/R-4.2.2/bin/exec
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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mkdir -p -- /usr/src/RPM/BUILD/R-4.2.2/lib
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rmain.c -o Rmain.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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x86_64-alt-linux-gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -L/usr/local/lib64 -o R.bin Rmain.o -lR
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
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making rbitmap.d from rbitmap.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
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making rotated.d from rotated.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
making Lapack.d from Lapack.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
making Rsock.d from Rsock.c
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making sock.d from sock.c
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making sockconn.d from sockconn.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
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making Rhttpd.d from Rhttpd.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
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making internet.d from internet.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
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making libcurl.d from libcurl.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
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making devX11.d from devX11.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rbitmap.c -o rbitmap.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Lapack.c -o Lapack.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rotated.c -o rotated.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o
libcurl.c: In function 'in_do_curlDownload':
libcurl.c:637:13: warning: 'CURLOPT_PROGRESSFUNCTION' is deprecated: since 7.32.0. Use CURLOPT_XFERINFOFUNCTION [-Wdeprecated-declarations]
637 | curl_easy_setopt(hnd[i], CURLOPT_PROGRESSFUNCTION, progress);
| ^~~~~~~~~~~~~~~~
In file included from libcurl.c:38:
/usr/include/curl/curl.h:1299:3: note: declared here
1299 | CURLOPTDEPRECATED(CURLOPT_PROGRESSFUNCTION, CURLOPTTYPE_FUNCTIONPOINT, 56,
| ^~~~~~~~~~~~~~~~~
libcurl.c:693:9: warning: 'CURLINFO_SIZE_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_SIZE_DOWNLOAD_T [-Wdeprecated-declarations]
693 | curl_easy_getinfo(hnd[0], CURLINFO_SIZE_DOWNLOAD, &dl);
| ^~~~~~~~~~~~~~~~~
/usr/include/curl/curl.h:2851:3: note: declared here
2851 | CURLINFO_SIZE_DOWNLOAD
| ^~~~~~~~~~~~~~~~~~~~~~
libcurl.c:702:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
702 | curl_easy_getinfo(hnd[0], CURLINFO_CONTENT_LENGTH_DOWNLOAD, &cl);
| ^~~~~~~~~~~~~~~~~
/usr/include/curl/curl.h:2868:3: note: declared here
2868 | CURLINFO_CONTENT_LENGTH_DOWNLOAD
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libcurl.c:714:13: warning: 'CURLINFO_SIZE_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_SIZE_DOWNLOAD_T [-Wdeprecated-declarations]
714 | curl_easy_getinfo(hnd[i], CURLINFO_SIZE_DOWNLOAD, &dl);
| ^~~~~~~~~~~~~~~~~
/usr/include/curl/curl.h:2851:3: note: declared here
2851 | CURLINFO_SIZE_DOWNLOAD
| ^~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dataentry.c -o dataentry.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devX11.c -o devX11.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o lapack.so Lapack.o -lR -llapack -lopenblas -lgfortran -lm -lquadmath
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
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mkdir -p -- /usr/src/RPM/BUILD/R-4.2.2/modules
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
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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 -lharfbuzz -lz -lpng16 -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o sock.o sockconn.o -lcurl -lR
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
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x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lpng16 -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library'
mkdir -p -- ../../library
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building system startup profile
mkdir -p -- ../../../library/base/R
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building package 'translations'
mkdir -p -- ../../../library/translations
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building package 'base'
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mkdir -p -- ../../../library/base/demo
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building package 'tools'
mkdir -p -- ../../../library/tools
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mkdir -p -- ../../../library/tools/R
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making md5.d from md5.c
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making init.d from init.c
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making text.d from text.c
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making http.d from http.c
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making pdscan.d from pdscan.c
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c patterns.c -o patterns.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clippath.c -o clippath.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stubs.c -o stubs.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devices.c -o devices.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mask.c -o mask.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c group.c -o group.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devPicTeX.c -o devPicTeX.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c colors.c -o colors.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devPS.c -o devPS.o
devPS.c: In function 'XFigDeviceDriver':
devPS.c:4950:53: warning: pointer 'pd_139' used after 'free' [-Wuse-after-free]
4950 | error(_("invalid page type '%s' (xfig)"), pd->papername);
| ~~^~~~~~~~~~~
devPS.c:4949:9: note: call to 'free' here
4949 | free(pd);
| ^~~~~~~~
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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 clippath.o patterns.o mask.o group.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
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making cairoBM.d from cairoBM.c
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x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cairoBM.c -o cairoBM.o
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x86_64-alt-linux-gcc -shared -L"../../../../../lib" -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lcairo -lpng16 -L"../../../../../lib" -lR -lm
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building package 'graphics'
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stem.c -o stem.o
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c base.c -o base.o
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c par.c -o par.o
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plot3d.c -o plot3d.o
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c graphics.c -o graphics.o
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plot.c -o plot.o
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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
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o
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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 -fopenmp -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR
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making gpar.d from gpar.c
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making grid.d from grid.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
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making just.d from just.c
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making layout.d from layout.c
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making mask.d from mask.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
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making matrix.d from matrix.c
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making path.d from path.c
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making register.d from register.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
making state.d from state.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
making unit.d from unit.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
making util.d from util.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
making viewport.d from viewport.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clippath.c -o clippath.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c just.c -o just.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mask.c -o mask.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c matrix.c -o matrix.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c register.c -o register.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c path.c -o path.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gpar.c -o gpar.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c util.c -o util.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c viewport.c -o viewport.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c layout.c -o layout.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c state.c -o state.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c unit.c -o unit.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c grid.c -o grid.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so clippath.o gpar.o grid.o just.o layout.o mask.o matrix.o path.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid'
byte-compiling package 'grid'
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building package 'splines'
mkdir -p -- ../../../library/splines
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mkdir -p -- ../../../library/splines/R
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making splines.d from splines.c
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c splines.c -o splines.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src'
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src'
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mkdir -p -- ../../../../library/splines/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src'
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byte-compiling package 'splines'
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
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mkdir -p -- ../../../library/stats4/R
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4'
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byte-compiling package 'stats4'
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
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mkdir -p -- ../../../library/tcltk/exec
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making init.d from init.c
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making tcltk_unix.d from tcltk_unix.c
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making tcltk.d from tcltk.c
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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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src'
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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tcltk_unix.c -o tcltk_unix.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src'
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 -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tcltk.c -o tcltk.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src'
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 -ltcl8.6 -lpthread -L/usr/lib64 -ltk8.6 -lX11 -lm -L../../../../lib -lR
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src'
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mkdir -p -- ../../../../library/tcltk/libs
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk'
byte-compiling package 'tcltk'
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
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making rngstream.d from rngstream.c
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making init.d from init.c
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making fork.d from fork.c
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make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rngstream.c -o rngstream.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fork.c -o fork.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
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[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel'
byte-compiling package 'parallel'
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library'
installing parsed NAMESPACE files
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make[1]: Nothing to be done for 'R'.
make: Entering directory '/usr/src/RPM/BUILD/R-4.2.2'
you should 'make docs' now ...
make: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2'
configuring Java ...
Java interpreter : /usr/lib/jvm/jre/bin/java
Java version : 17.0.8
Java home path : /usr/lib/jvm/jre
Java compiler : not present
Java headers gen.:
Java archive tool:
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L$(JAVA_HOME)/lib -ljvm
make[2]: Entering directory '/usr/src/tmp/Rjavareconf.dRGYds'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: jni.h: No such file or directory
1 | #include <jni.h>
| ^~~~~~~
compilation terminated.
make[2]: *** [/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf:169: conftest.o] Error 1
make[2]: Leaving directory '/usr/src/tmp/Rjavareconf.dRGYds'
Unable to compile a JNI program
JAVA_HOME : /usr/lib/jvm/jre
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/src/RPM/BUILD/R-4.2.2
Done.
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2'
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creating doc/NEWS
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creating doc/NEWS.pdf
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creating doc/manual/version.texi
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creating doc/manual/R-FAQ.html
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creating doc/manual/R-data.html
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creating doc/manual/R-lang.html
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creating doc/manual/R-ints.html
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creating doc/manual/R-admin.html
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creating doc/manual/R-intro.html
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make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library'
building/updating vignettes for package 'grid' ...
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
building/updating vignettes for package 'stats' ...
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toeplitz html
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var.test html
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weights html
wilcox.test html
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xtabs html
zC html
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BJsales html
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HairEyeColor html
Harman23.cor html
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airquality html
anscombe html
attenu html
attitude html
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beavers html
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datasets-package html
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faithful html
freeny html
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islands html
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longley html
lynx html
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mtcars html
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state html
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trees html
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women html
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converting help for package 'grid'
Grid html
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dataViewport html
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deviceLoc html
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grid.show.viewport html
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unit.c html
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converting help for package 'splines'
asVector html
backSpline html
bs html
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ns html
periodicSpline html
polySpline html
predict.bSpline html
predict.bs html
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converting help for package 'stats4'
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converting help for package 'tcltk'
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converting help for package 'compiler'
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converting help for package 'parallel'
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make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package MASS
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begin installing recommended package lattice
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
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begin installing recommended package foreign
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package KernSmooth
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make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package nnet
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package spatial
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'codetools' ...
** package 'codetools' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'codetools'
finding HTML links ... done
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codetools html
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Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'nnet' ...
** package 'nnet' successfully unpacked and MD5 sums checked
** using non-staged installation
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make[3]: Entering directory '/usr/src/tmp/Rtmpn1V4pt/R.INSTALL3c6bcc22ebaa54/nnet/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nnet.c -o nnet.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpn1V4pt/R.INSTALL3c6bcc22ebaa54/nnet/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpn1V4pt/R.INSTALL3c6bcc22ebaa54/nnet/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmpn1V4pt/R.INSTALL3c6bcc22ebaa54/nnet/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/library/nnet/libs
** R
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** 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
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nnet html
predict.nnet html
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** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
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* installing *source* package 'spatial' ...
** package 'spatial' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pps.c -o pps.o
make[3]: Leaving directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c krc.c -o krc.o
make[3]: Leaving directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmppwQgCv/R.INSTALL3c6bcb72569fcf/spatial/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cp.f -o cp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgefa.f -o dgefa.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgedi.f -o dgedi.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c linbin2D.f -o linbin2D.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c blkest.f -o blkest.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c linbin.f -o linbin.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgesl.f -o dgesl.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c locpoly.f -o locpoly.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rlbin.f -o rlbin.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sstdiag.f -o sstdiag.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sdiag.f -o sdiag.o
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/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-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpttqTh5/R.INSTALL3c6bcfce7263c/KernSmooth/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'foreign' ...
** package 'foreign' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c avl.c -o avl.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c file-handle.c -o file-handle.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c format.c -o format.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c R_systat.c -o R_systat.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c SASxport.c -o SASxport.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dbfopen.c -o dbfopen.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c minitab.c -o minitab.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pfm-read.c -o pfm-read.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c spss.c -o spss.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stataread.c -o stataread.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sfm-read.c -o sfm-read.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/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-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpYjwMKE/R.INSTALL3c6bc84cf1f09a/foreign/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'rpart' ...
** package 'rpart' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c anovapred.c -o anovapred.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c branch.c -o branch.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bsplit.c -o bsplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fix_cp.c -o fix_cp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c anova.c -o anova.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c choose_surg.c -o choose_surg.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c free_tree.c -o free_tree.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c graycode.c -o graycode.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gini.c -o gini.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c insert_split.c -o insert_split.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mysort.c -o mysort.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c partition.c -o partition.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nodesplit.c -o nodesplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c print_tree.c -o print_tree.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c poisson.c -o poisson.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpartexp.c -o rpartexp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpart.c -o rpart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpcountup.c -o rpcountup.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rundown.c -o rundown.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rundown2.c -o rundown2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c usersplit.c -o usersplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c surrogate.c -o surrogate.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c xval.c -o xval.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c xpred.c -o xpred.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/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-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpaBjN4c/R.INSTALL3c6bc7171935e2/rpart/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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.balance html
stagec html
summary.rpart html
text.rpart html
xpred.rpart html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpjroP95/R.INSTALL3c6bba6400cd2a/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c MASS.c -o MASS.o
make[3]: Leaving directory '/usr/src/tmp/RtmpjroP95/R.INSTALL3c6bba6400cd2a/MASS/src'
make[3]: Entering directory '/usr/src/tmp/RtmpjroP95/R.INSTALL3c6bba6400cd2a/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lqs.c -o lqs.o
make[3]: Leaving directory '/usr/src/tmp/RtmpjroP95/R.INSTALL3c6bba6400cd2a/MASS/src'
make[3]: Entering directory '/usr/src/tmp/RtmpjroP95/R.INSTALL3c6bba6400cd2a/MASS/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpjroP95/R.INSTALL3c6bba6400cd2a/MASS/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
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
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package cluster
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package class
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'class' ...
** package 'class' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpMN9Hn7/R.INSTALL3cb59f1fff85f/class/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c class.c -o class.o
make[3]: Leaving directory '/usr/src/tmp/RtmpMN9Hn7/R.INSTALL3cb59f1fff85f/class/src'
make[3]: Entering directory '/usr/src/tmp/RtmpMN9Hn7/R.INSTALL3cb59f1fff85f/class/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpMN9Hn7/R.INSTALL3cb59f1fff85f/class/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'lattice' ...
** package 'lattice' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpN9uGNo/R.INSTALL3c6bc42cfecd78/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpN9uGNo/R.INSTALL3c6bc42cfecd78/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpN9uGNo/R.INSTALL3c6bc42cfecd78/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c threeDplot.c -o threeDplot.o
make[3]: Leaving directory '/usr/src/tmp/RtmpN9uGNo/R.INSTALL3c6bc42cfecd78/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpN9uGNo/R.INSTALL3c6bc42cfecd78/lattice/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpN9uGNo/R.INSTALL3c6bc42cfecd78/lattice/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package Matrix
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package nlme
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'cluster' ...
** package 'cluster' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dysta.f -o dysta.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c daisy.f -o daisy.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c spannel.c -o spannel.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sildist.c -o sildist.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mona.c -o mona.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fanny.c -o fanny.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c twins.c -o twins.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clara.c -o clara.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pam.c -o pam.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/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-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmpha40Re/R.INSTALL3cb59b76acb735/cluster/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
clusplot.partition html
cluster-internal html
coef.hclust html
daisy html
diana html
dissimilarity.object html
ellipsoidhull html
fanny html
fanny.object html
flower html
lower.to.upper.tri.inds html
medoids html
mona html
mona.object html
pam html
pam.object html
partition.object html
plantTraits html
plot.agnes html
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
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
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chol.f -o chol.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pythag.c -o pythag.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pdMat.c -o pdMat.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rs.f -o rs.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gnls.c -o gnls.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c matrix.c -o matrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nlme.c -o nlme.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c corStruct.c -o corStruct.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nlmefit.c -o nlmefit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/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 pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpQLeNUn/R.INSTALL3cc0ac6b5d8682/nlme/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/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
varConstProp html
varExp html
varFixed html
varFunc html
varIdent html
varPower html
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varWeights.lmeStruct html
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Tsparse.c -o Tsparse.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cs_utils.c -o cs_utils.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c CHMfactor.c -o CHMfactor.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgTMatrix.c -o dgTMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c TMatrix_as.c -o TMatrix_as.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpoMatrix.c -o dpoMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgCMatrix.c -o dgCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dppMatrix.c -o dppMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dsCMatrix.c -o dsCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chm_common.c -o chm_common.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dsyMatrix.c -o dsyMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtTMatrix.c -o dtTMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgeMatrix.c -o dgeMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtCMatrix.c -o dtCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dspMatrix.c -o dspMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtrMatrix.c -o dtrMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
( cd Lib ; make clean )
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ldense.c -o ldense.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtpMatrix.c -o dtpMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c factorizations.c -o factorizations.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
( cd Source ; make clean )
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Csparse.c -o Csparse.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c abIndex.c -o abIndex.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lgCMatrix.c -o lgCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
( cd Source ; make clean )
( cd Lib ; make -f "/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf" -f Makefile )
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparseQR.c -o sparseQR.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:275:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
275 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
../Core/cholmod_copy.c:275:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
275 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cs.c -o cs.o
cs.c: In function 'cs_realloc':
cs.c:1161:26: warning: pointer 'p_11(D)' may be used after 'realloc' [-Wuse-after-free]
1161 | return ((*ok) ? pnew : p) ; /* return original p if failure */
| ~~~~~~~~~~~~~~^~~~
cs.c:1159:12: note: call to 'realloc' here
1159 | pnew = realloc (p, CS_MAX (n,1) * size) ; /* realloc the block */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c unpackedMatrix.c -o unpackedMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_memory.c -o cholmod_memory.o
../Core/cholmod_memory.c: In function 'cholmod_malloc':
../Core/cholmod_memory.c:121:12: warning: unused variable 's' [-Wunused-variable]
121 | size_t s ;
| ^
../Core/cholmod_memory.c: In function 'cholmod_realloc':
../Core/cholmod_memory.c:311:12: warning: unused variable 's' [-Wunused-variable]
311 | size_t s ;
| ^
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:45:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
In file included from ../Core/cholmod_dense.c:47:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
In file included from ../Core/cholmod_dense.c:49:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:300:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
300 | Int i, n, nz ;
| ^~
../Core/cholmod_dense.c:299:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
299 | double *Xx, *Xz ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse':
../Core/cholmod_sparse.c:485:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
485 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
| ^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:113:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
37 | double *Lx, *Lz ;
| ^~
In file included from ../Core/cholmod_change_factor.c:115:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
37 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:262:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
262 | Int nsuper, xsize, ssize ;
| ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:677:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
677 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:677:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
677 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:676:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
676 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c:676:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
676 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:824:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
824 | Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
| ^
../Core/cholmod_change_factor.c:823:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~~
../Core/cholmod_change_factor.c:823:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Mutils.c -o Mutils.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:105:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:107:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:109:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:342:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
342 | Int i, j, p, k, stype, nrow, ncol, nz, ok ;
| ^~
../Core/cholmod_triplet.c:341:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
341 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:419:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
419 | Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
| ^~~~
../Cholesky/cholmod_analyze.c:416:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
../Cholesky/cholmod_analyze.c:416:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p':
../Cholesky/cholmod_factorize.c:111:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
111 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
| ^
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:366:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
366 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:121:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:123:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:125:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:130:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | 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:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | 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:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c packedMatrix.c -o packedMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:204:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
204 | Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
| ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:950:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
950 | Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
| ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1497:9: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
1497 | ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
| ^~~
../Check/cholmod_check.c:1495:16: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
1495 | count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
| ^~~~~~~
../Check/cholmod_check.c:1494:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
1494 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dense.c -o dense.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:161:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:163:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:165:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:169:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:171:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:173:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o
../Core/cholmod_add.c:34:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
34 | double alpha [2], /* scale factor for A */
| ~~~~~~~^~~~~~~~~
In file included from ../Core/cholmod_add.c:27:
../Include/cholmod_core.h:1582:68: note: previously declared as 'double *'
1582 | cholmod_sparse *cholmod_l_add (cholmod_sparse *, cholmod_sparse *, double *,
| ^~~~~~~~
../Core/cholmod_add.c:35:12: warning: argument 4 of type 'double[2]' with mismatched bound [-Warray-parameter=]
35 | double beta [2], /* scale factor for B */
| ~~~~~~~^~~~~~~~
../Include/cholmod_core.h:1583:5: note: previously declared as 'double *'
1583 | double *, int, int, cholmod_common *) ;
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:562:21: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
562 | Int totsize ;
| ^~~~~~~
../Supernodal/cholmod_super_symbolic.c:185:12: warning: unused variable 'max_fraction' [-Wunused-variable]
185 | double max_fraction;
| ^~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:184:17: warning: unused variable 'env_max_fraction' [-Wunused-variable]
184 | const char* env_max_fraction;
| ^~~~~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:183:12: warning: unused variable 'max_bytes' [-Wunused-variable]
183 | size_t max_bytes;
| ^~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:182:17: warning: unused variable 'env_max_bytes' [-Wunused-variable]
182 | const char* env_max_bytes;
| ^~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:181:17: warning: unused variable 'env_use_gpu' [-Wunused-variable]
181 | const char* env_use_gpu;
| ^~~~~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:26:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
30 | 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:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
238 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
30 | 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:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
238 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:82:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
756 | #pragma omp parallel for private ( j, i, px, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
116 | tail, nscol_new = 0;
| ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
111 | *Previous;
| ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
In file included from ../Supernodal/cholmod_super_numeric.c:84:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
756 | #pragma omp parallel for private ( j, i, px, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
116 | tail, nscol_new = 0;
| ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
111 | *Previous;
| ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
In file included from ../Supernodal/cholmod_super_numeric.c:86:
../Supernodal/t_cholmod_super_numeric.c: In function 'z_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
756 | #pragma omp parallel for private ( j, i, px, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
116 | tail, nscol_new = 0;
| ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
111 | *Previous;
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o
../Core/cholmod_copy.c: In function 'cholmod_l_copy':
../Core/cholmod_copy.c:275:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
275 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
../Core/cholmod_copy.c:275:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
275 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o
../Core/cholmod_memory.c: In function 'cholmod_l_malloc':
../Core/cholmod_memory.c:121:12: warning: unused variable 's' [-Wunused-variable]
121 | size_t s ;
| ^
../Core/cholmod_memory.c: In function 'cholmod_l_realloc':
../Core/cholmod_memory.c:311:12: warning: unused variable 's' [-Wunused-variable]
311 | size_t s ;
| ^
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:485:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
485 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
| ^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:45:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
In file included from ../Core/cholmod_dense.c:47:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
In file included from ../Core/cholmod_dense.c:49:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
27 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
133 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
226 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:300:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
300 | Int i, n, nz ;
| ^~
../Core/cholmod_dense.c:299:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
299 | double *Xx, *Xz ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:44:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
In file included from ../MatrixOps/cholmod_sdmult.c:48:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:113:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
37 | double *Lx, *Lz ;
| ^~
In file included from ../Core/cholmod_change_factor.c:115:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
37 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:262:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
262 | Int nsuper, xsize, ssize ;
| ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:677:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
677 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:677:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
677 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:676:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
676 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c:676:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
676 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:824:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
824 | Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
| ^
../Core/cholmod_change_factor.c:823:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~~
../Core/cholmod_change_factor.c:823:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:105:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:107:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:109:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
28 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:342:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
342 | Int i, j, p, k, stype, nrow, ncol, nz, ok ;
| ^~
../Core/cholmod_triplet.c:341:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
341 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:366:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
366 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2':
../Cholesky/cholmod_analyze.c:419:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
419 | Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
| ^~~~
../Cholesky/cholmod_analyze.c:416:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
../Cholesky/cholmod_analyze.c:416:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c:101:12: warning: argument 2 of type 'double[2]' with mismatched bound [-Warray-parameter=]
101 | double beta [2], /* factorize beta*I+A or beta*I+A'*A */
| ~~~~~~~^~~~~~~~
In file included from ../Cholesky/cholmod_factorize.c:58:
../Include/cholmod_cholesky.h:168:46: note: previously declared as 'double *'
168 | int cholmod_l_factorize_p (cholmod_sparse *, double *, SuiteSparse_long *,
| ^~~~~~~~
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:111:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
111 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
| ^
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
In file included from ../Core/cholmod_transpose.c:121:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:123:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:125:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
42 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
139 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:130:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | 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:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
43 | 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:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_solve.c:63:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
61 | double *Lx, *Yx, *Yz ;
| ^~
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
61 | double *Lx, *Yx, *Yz ;
| ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:334:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
334 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:204:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
204 | Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
| ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:950:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
950 | Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
| ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1497:9: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
1497 | ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
| ^~~
../Check/cholmod_check.c:1495:16: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
1495 | count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
| ^~~~~~~
../Check/cholmod_check.c:1494:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
1494 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
../Modify/cholmod_rowdel.c:72:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
72 | double yk [2], /* kth entry in the solution to A*y=b */
| ~~~~~~~^~~~~~
In file included from ../Modify/cholmod_rowdel.c:25:
../Include/cholmod_modify.h:294:55: note: previously declared as 'double *'
294 | int cholmod_l_rowdel_solve (size_t, cholmod_sparse *, double *,
| ^~~~~~~~
../Modify/cholmod_rowdel.c:104:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
104 | double yk [2], /* kth entry in the solution to A*y=b */
| ~~~~~~~^~~~~~
../Include/cholmod_modify.h:320:54: note: previously declared as 'double *'
320 | int cholmod_l_rowdel_mark (size_t, cholmod_sparse *, double *,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparse.c -o sparse.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
../Modify/cholmod_rowadd.c:72:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
72 | double bk [2], /* kth entry of the right-hand-side b */
| ~~~~~~~^~~~~~
In file included from ../Modify/cholmod_rowadd.c:24:
../Include/cholmod_modify.h:215:55: note: previously declared as 'double *'
215 | int cholmod_l_rowadd_solve (size_t, cholmod_sparse *, double *,
| ^~~~~~~~
../Modify/cholmod_rowadd.c:116:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
116 | double bk [2], /* kth entry of the right hand side, b */
| ~~~~~~~^~~~~~
../Include/cholmod_modify.h:241:54: note: previously declared as 'double *'
241 | int cholmod_l_rowadd_mark (size_t, cholmod_sparse *, double *,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:161:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:163:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:165:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:169:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:171:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:173:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/cholmod_rowfac.c: At top level:
../Cholesky/cholmod_rowfac.c:577:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
577 | double beta [2], /* factorize beta*I+A or beta*I+AA' */
| ~~~~~~~^~~~~~~~
In file included from ../Cholesky/cholmod_rowfac.c:103:
../Include/cholmod_cholesky.h:387:59: note: previously declared as 'double *'
387 | int cholmod_l_rowfac (cholmod_sparse *, cholmod_sparse *, double *, size_t,
| ^~~~~~~~
../Cholesky/cholmod_rowfac.c:602:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
602 | double beta [2], /* factorize beta*I+A or beta*I+AA' */
| ~~~~~~~^~~~~~~~
../Include/cholmod_cholesky.h:413:64: note: previously declared as 'double *'
413 | int cholmod_l_rowfac_mask (cholmod_sparse *, cholmod_sparse *, double *, size_t,
| ^~~~~~~~
../Cholesky/cholmod_rowfac.c:629:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
629 | double beta [2], /* factorize beta*I+A or beta*I+AA' */
| ~~~~~~~^~~~~~~~
../Include/cholmod_cholesky.h:434:65: note: previously declared as 'double *'
434 | int cholmod_l_rowfac_mask2 (cholmod_sparse *, cholmod_sparse *, double *,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:562:21: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
562 | Int totsize ;
| ^~~~~~~
../Supernodal/cholmod_super_symbolic.c:185:12: warning: unused variable 'max_fraction' [-Wunused-variable]
185 | double max_fraction;
| ^~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:184:17: warning: unused variable 'env_max_fraction' [-Wunused-variable]
184 | const char* env_max_fraction;
| ^~~~~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:183:12: warning: unused variable 'max_bytes' [-Wunused-variable]
183 | size_t max_bytes;
| ^~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:182:17: warning: unused variable 'env_max_bytes' [-Wunused-variable]
182 | const char* env_max_bytes;
| ^~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:181:17: warning: unused variable 'env_use_gpu' [-Wunused-variable]
181 | const char* env_use_gpu;
| ^~~~~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -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:26:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
30 | 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:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
238 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
30 | 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:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
238 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:82:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
756 | #pragma omp parallel for private ( j, i, px, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
116 | tail, nscol_new = 0;
| ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
111 | *Previous;
| ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
In file included from ../Supernodal/cholmod_super_numeric.c:84:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
756 | #pragma omp parallel for private ( j, i, px, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
116 | tail, nscol_new = 0;
| ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
111 | *Previous;
| ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
In file included from ../Supernodal/cholmod_super_numeric.c:86:
../Supernodal/t_cholmod_super_numeric.c: In function 'z_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
|
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
756 | #pragma omp parallel for private ( j, i, px, q ) \
|
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
116 | tail, nscol_new = 0;
| ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
111 | *Previous;
| ^~~~~~~~
../Supernodal/cholmod_super_numeric.c: At top level:
../Supernodal/cholmod_super_numeric.c:102:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
102 | double beta [2], /* beta*I is added to diagonal of matrix to factorize */
| ~~~~~~~^~~~~~~~
In file included from ../Supernodal/cholmod_super_numeric.c:60:
../Include/cholmod_supernodal.h:120:66: note: previously declared as 'double *'
120 | int cholmod_l_super_numeric (cholmod_sparse *, cholmod_sparse *, double *,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:44:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
In file included from ../MatrixOps/cholmod_sdmult.c:48:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/cholmod_sdmult.c: At top level:
../MatrixOps/cholmod_sdmult.c:59:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
59 | double alpha [2], /* scale factor for A */
| ~~~~~~~^~~~~~~~~
In file included from ../MatrixOps/cholmod_sdmult.c:36:
../Include/cholmod_matrixops.h:143:46: note: previously declared as 'double *'
143 | int cholmod_l_sdmult (cholmod_sparse *, int, double *, double *,
| ^~~~~~~~
../MatrixOps/cholmod_sdmult.c:60:12: warning: argument 4 of type 'double[2]' with mismatched bound [-Warray-parameter=]
60 | double beta [2], /* scale factor for Y */
| ~~~~~~~^~~~~~~~
../Include/cholmod_matrixops.h:143:56: note: previously declared as 'double *'
143 | int cholmod_l_sdmult (cholmod_sparse *, int, double *, double *,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:63:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
61 | double *Lx, *Yx, *Yz ;
| ^~
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
61 | double *Lx, *Yx, *Yz ;
| ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:334:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
334 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask2':
../Modify/cholmod_updown.c:433:40: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
433 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
| ^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask2':
../Modify/cholmod_updown.c:433:40: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
433 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
| ^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
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
ar: `u' modifier ignored since `D' is the default (see `U')
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/CHOLMOD/Lib'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c colamd.c -o colamd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c colamd.c -o colamd_l.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/COLAMD/Source'
ar -rucs ../../COLAMD.a colamd.o colamd_l.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/COLAMD/Source'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_1.c -o amd_i_1.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_order.c -o amd_i_order.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_control.c -o amd_i_control.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_2.c -o amd_i_2.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_info.c -o amd_i_info.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
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
ar: `u' modifier ignored since `D' is the default (see `U')
make[5]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/AMD/Source'
make[4]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c SuiteSparse_config.c -o SuiteSparse_config.o
make[4]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/SuiteSparse_config'
make[4]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/SuiteSparse_config'
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src/SuiteSparse_config'
make[3]: Entering directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/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 packedMatrix.o unpackedMatrix.o sparse.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpLCHQ0A/R.INSTALL3cc0a93577ea90/Matrix/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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'
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
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.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csc","RsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': 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.coo","RsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","sparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","sparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","sparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': 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 '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"Matrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"Matrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"Matrix","matrix.coo"': no definition for class "matrix.coo"
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 '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'
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'
in method for 'coerce' with signature '"graphAM","TsparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","RsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","TsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","sparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"Matrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"Matrix","graph"': no definition for class "graph"
Creating a generic function for 'diag<-' 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'
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'
Creating a generic function for 'which' from package 'base' 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
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
dmperm 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
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
mat2triplet html
matrix-products html
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
packedMatrix-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
unpackedMatrix-class html
unused-classes html
updown html
wrld_1deg html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package mgcv
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package survival
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'survival' ...
** package 'survival' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agsurv5.c -o agsurv5.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agsurv4.c -o agsurv4.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agmart.c -o agmart.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agmart3.c -o agmart3.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agscore2.c -o agscore2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agsurv3.c -o agsurv3.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agexact.c -o agexact.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cholesky2.c -o cholesky2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chinv2.c -o chinv2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cdecomp.c -o cdecomp.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chinv3.c -o chinv3.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agfit5.c -o agfit5.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agfit4.c -o agfit4.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cholesky3.c -o cholesky3.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cholesky5.c -o cholesky5.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chsolve5.c -o chsolve5.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chsolve2.c -o chsolve2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chsolve3.c -o chsolve3.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c collapse.c -o collapse.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c concordance1.c -o concordance1.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxcount1.c -o coxcount1.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c concordance5.c -o concordance5.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxdetail.c -o coxdetail.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxsafe.c -o coxsafe.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c concordance3.c -o concordance3.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxmart.c -o coxmart.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxmart2.c -o coxmart2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxexact.c -o coxexact.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxfit6.c -o coxfit6.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxfit5.c -o coxfit5.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxscho.c -o coxscho.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxscore2.c -o coxscore2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxsurv1.c -o coxsurv1.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dmatrix.c -o dmatrix.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c doloop.c -o doloop.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxsurv2.c -o coxsurv2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c finegray.c -o finegray.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gchol.c -o gchol.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c multicheck.c -o multicheck.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c norisk.c -o norisk.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pyears2.c -o pyears2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pyears1.c -o pyears1.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pystep.c -o pystep.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pyears3b.c -o pyears3b.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survConcordance.c -o survConcordance.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survdiff2.c -o survdiff2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfit4.c -o survfit4.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfitci.c -o survfitci.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survpenal.c -o survpenal.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survreg6.c -o survreg6.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survreg7.c -o survreg7.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfitresid.c -o survfitresid.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survregc1.c -o survregc1.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survregc2.c -o survregc2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfitkm.c -o survfitkm.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survsplit.c -o survsplit.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tmerge.c -o tmerge.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c zph1.c -o zph1.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c zph2.c -o zph2.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agsurv3.o agsurv4.o agsurv5.o cdecomp.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o collapse.o concordance1.o concordance3.o concordance5.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore2.o coxsurv1.o coxsurv2.o dmatrix.o doloop.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o zph1.o zph2.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmpt4TOVZ/R.INSTALL3dedf572ec09bb/survival/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/library/survival/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 'survival'
finding HTML links ... done
Surv html
Surv2 html
Surv2data html
Survmethods html
aareg html
aeqSurv html
aggregate.survfit html
agreg.fit html
aml html
anova.coxph html
attrassign html
basehaz html
bladder html
blogit html
cch html
cgd html
cgd0 html
cipoisson html
clogit html
cluster html
colon html
concordance html
concordancefit html
cox.zph html
coxph html
coxph.control html
coxph.detail html
coxph.object html
coxph.wtest html
coxphms.object html
coxsurv.fit html
diabetic html
dsurvreg html
finegray html
flchain html
frailty html
gbsg html
heart html
is.ratetable html
kidney html
levels.Surv html
lines.survfit html
logLik.coxph html
logan html
lung html
mgus html
mgus2 html
model.frame.coxph html
model.matrix.coxph html
myeloid html
myeloma html
nafld html
neardate html
nsk html
nwtco html
ovarian html
pbc html
pbcseq html
plot.aareg html
plot.cox.zph html
plot.survfit html
predict.coxph html
predict.survreg html
print.aareg html
print.summary.coxph html
print.summary.survexp html
print.summary.survfit html
print.survfit html
pseudo html
pspline html
pyears html
quantile.survfit html
ratetable html
ratetableDate html
rats html
rats2 html
reliability html
residuals.coxph html
residuals.survfit html
residuals.survreg html
retinopathy html
rhDNase html
ridge html
rotterdam html
royston html
rttright html
solder html
stanford2 html
statefig html
strata html
summary.aareg html
summary.coxph html
summary.pyears html
summary.survexp html
summary.survfit html
survSplit html
survcheck html
survdiff html
survexp html
survexp.fit html
survexp.object html
survexp.us html
survfit html
survfit.coxph html
survfit.formula html
survfit.matrix html
survfit.object html
survfit0 html
survfitcoxph.fit html
survival-deprecated html
survival-internal html
survobrien html
survreg html
survreg.control html
survreg.distributions html
survreg.object html
survregDtest html
tcut html
tmerge html
tobin html
transplant html
udca html
untangle.specials html
uspop2 html
vcov.coxph html
veteran html
xtfrm.Surv html
yates html
yates_setup html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
begin installing recommended package boot
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'boot' ...
** package 'boot' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'boot'
finding HTML links ... done
EEF.profile html
Imp.Estimates html
abc.ci html
acme html
aids html
aircondit html
amis html
aml html
beaver html
bigcity html
boot-practicals html
boot html
boot.array html
boot.ci html
brambles html
breslow html
calcium html
cane html
capability html
catsM html
cav html
cd4 html
cd4.nested html
censboot html
channing html
claridge html
cloth html
co.transfer html
coal html
control html
corr html
cum3 html
cv.glm html
darwin html
dogs html
downs.bc html
ducks html
empinf html
envelope html
exp.tilt html
fir html
freq.array html
frets html
glm.diag html
glm.diag.plots html
gravity html
hirose html
imp.weights html
inv.logit html
islay html
jack.after.boot html
k3.linear html
linear.approx html
lines.saddle.distn html
logit html
manaus html
melanoma html
motor html
neuro html
nitrofen html
nodal html
norm.ci html
nuclear html
paulsen html
plot.boot html
poisons html
polar html
print.boot html
print.bootci html
print.saddle.distn html
print.simplex html
remission html
saddle html
saddle.distn html
saddle.distn.object html
salinity html
simplex html
simplex.object html
smooth.f html
sunspot html
survival html
tau html
tilt.boot html
tsboot html
tuna html
urine html
var.linear html
wool html
** building package indices
** testing if installed package can be loaded
* DONE (boot)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended'
* installing *source* package 'mgcv' ...
** package 'mgcv' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c davies.c -o davies.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxph.c -o coxph.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c soap.c -o soap.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mvn.c -o mvn.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c misc.c -o misc.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mgcv.c -o mgcv.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qp.c -o qp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c magic.c -o magic.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c matrix.c -o matrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparse-smooth.c -o sparse-smooth.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tprs.c -o tprs.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparse.c -o sparse.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c discrete.c -o discrete.o
discrete.c: In function 'XWXijspace':
discrete.c:1074:11: warning: unused variable 'kk' [-Wunused-variable]
1074 | jm,im,kk,ddtj,
| ^~
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gdi.c -o gdi.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ncv.c -o ncv.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mat.c -o mat.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o ncv.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -fopenmp -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: warning: type of 'dtrsm_' does not match original declaration [-Wlto-type-mismatch]
216 | F77_NAME(dtrsm)(const char *side, const char *uplo,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: note: type mismatch in parameter 12
216 | F77_NAME(dtrsm)(const char *side, const char *uplo,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: note: type 'size_t' should match type 'void'
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: note: 'dtrsm_' was previously declared here
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: warning: type of 'dsyrk_' does not match original declaration [-Wlto-type-mismatch]
242 | F77_NAME(dsyrk)(const char *uplo, const char *trans,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: note: type mismatch in parameter 11
242 | F77_NAME(dsyrk)(const char *uplo, const char *trans,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: note: type 'size_t' should match type 'void'
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: note: 'dsyrk_' was previously declared here
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: warning: type of 'dtrmm_' does not match original declaration [-Wlto-type-mismatch]
225 | F77_NAME(dtrmm)(const char *side, const char *uplo, const char *transa,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: note: type mismatch in parameter 12
225 | F77_NAME(dtrmm)(const char *side, const char *uplo, const char *transa,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: note: type 'size_t' should match type 'void'
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: note: 'dtrmm_' was previously declared here
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: warning: type of 'dgemm_' does not match original declaration [-Wlto-type-mismatch]
207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: note: type mismatch in parameter 14
207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: note: type 'size_t' should match type 'void'
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: note: 'dgemm_' was previously declared here
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: warning: type of 'dgemv_' does not match original declaration [-Wlto-type-mismatch]
107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: note: type mismatch in parameter 12
107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
| ^
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: note: type 'size_t' should match type 'void'
/usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: note: 'dgemv_' was previously declared here
make[3]: Leaving directory '/usr/src/tmp/RtmpYGFHHs/R.INSTALL3dedf3dd1ecfd/mgcv/src'
installing to /usr/src/RPM/BUILD/R-4.2.2/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mgcv'
finding HTML links ... done
Beta html
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** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
Making 'packages.html' ... done
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[]@textrm The tar-balls are avail-able from [][]@texttt https:// stat. ethz.
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[]@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de
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[]@textrm The tar-balls are avail-able from [][]@texttt https:// stat. ethz.
ch/ R/ daily/ [][][]@textrm . Down-load
[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14]
Chapter 3 [15] [16]
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[]@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de
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[26]
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[27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35]
[36] Appendix A [37] [38] [39]
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[40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Appendix B [50] [51] [52]
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[62]
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[65] [66] [67] [68]
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[69] (Function and variable index) [70]
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@textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd
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[3] [4] [5] [6]
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[]@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics''
.
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@textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7,
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[][]@texttt https:// master. bioconductor. org/ help/ publications/ book
s/
[7]
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@textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/
10. 1080/ 10618600. 1996.
[8] [9] [10] Chapter 3 [11] [12] [13] [14] [15] [16] [17] [18]
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[]@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra
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@texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia
l-ized ver-sions of
Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
Writing index file R-FAQ.fn
[39]
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@textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy
ch @textrm (@texttt https:// CRAN. R-project. org/
[40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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@textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd
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[3] [4] [5] [6]
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[]@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics''
.
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@textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7,
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[][]@texttt https:// master. bioconductor. org/ help/ publications/ book
s/
[7]
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@textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/
10. 1080/ 10618600. 1996.
[8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18]
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[]@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra
mming_language#
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@texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia
l-ized ver-sions of
Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
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[39]
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@textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy
ch @textrm (@texttt https:// CRAN. R-project. org/
[40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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[3] [4] [5] [6]
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[]@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics''
.
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@textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7,
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[][]@texttt https:// master. bioconductor. org/ help/ publications/ book
s/
[7]
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@textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/
10. 1080/ 10618600. 1996.
[8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18]
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mming_language#
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@texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia
l-ized ver-sions of
Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
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[39]
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@textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy
ch @textrm (@texttt https:// CRAN. R-project. org/
[40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14]
[15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23]
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Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14]
[15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23]
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[17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27]
[28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36]
[37] [38] [39] [40] [41] [42] [43] Chapter 7 [44]
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[45] Chapter 8 [46]
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[47]
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hoice of
[48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Chapter 9 [59] [60]
Chapter 10 [61] Chapter 11 [62] Chapter 12 [63] [64]
(Function and variable index) [65]
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atrix 1.2-6[]
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[] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[]
[17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27]
[28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36]
[37] [38] [39] [40] [41] [42] [43] Chapter 7 [44]
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@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
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@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a
sym-bolic link, as
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@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[45] Chapter 8 [46]
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[]@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http
s:// CRAN. R-project. org/
[47]
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@textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Chapter 9 [59] [60]
Chapter 10 [61] Chapter 11 [62] Chapter 12 [63] [64]
(Function and variable index) [65]
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.vrs [66]) (Concept index)
[67] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.cps) [68] )
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[] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M
atrix 1.2-6[]
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[] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[]
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[] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops'
(group)generic[]
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[] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[]
[17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27]
[28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36]
[37] [38] [39] [40] [41] [42] [43] Chapter 7 [44]
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@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
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@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a
sym-bolic link, as
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@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[45] Chapter 8 [46]
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[]@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http
s:// CRAN. R-project. org/
[47]
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@textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Chapter 9 [59] [60]
Chapter 10 [61] Chapter 11 [62] Chapter 12 [63] [64]
(Function and variable index) [65]
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.vrs [66]) (Concept index)
[67] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.cps) [68] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
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[55] )
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(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.vrs [52]) (Concept Index)
[53] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.cps) Appendix A [54]
[55] )
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[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93]
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[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13]
[14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24]
Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] </us
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4.2.2/doc/manual/images/ecdf.pdf> </usr/src/RPM/BUILD/R-4.2.2/doc/manual/images
/QQ.pdf> [35] [36] </usr/src/RPM/BUILD/R-4.2.2/doc/manual/images/ice.pdf>
[37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47]
[48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60]
[61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] </usr/src/RPM/BUIL
D/R-4.2.2/doc/manual/images/fig11.pdf> [71] </usr/src/RPM/BUILD/R-4.2.2/doc/man
ual/images/fig12.pdf> [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14
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[90] Appendix C [91] [92] Appendix D [93]
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[19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29]
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[69] [70] [71] [72] [73]
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[]@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro
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Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86]
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[88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4
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[]@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
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[158] Chapter 6 [159] [160] [161] [162] [163] [164] [165]
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[]@textrm Passing a variable-length string from C to For-tran is trick-ier, but
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[][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d
ocumentation/
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@texttt mixed-language-programming/ standard-tools-for-interoperability/ bind
. html[][][]
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Chapter 7 [182] [183] Chapter 8 [184] [185] [186]
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(see the transcript file for additional information)</usr/share/texmf-dist/font
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public/amsfonts/cm/cmr7.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr8.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></us
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ype1/public/amsfonts/cm/cmss10.pfb></usr/share/texmf-dist/fonts/type1/public/am
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re/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf-dist/
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lic/amsfonts/cm/cmtt10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/c
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[30] [31] [32]
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/ std/ standing-documents/
[33]
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[] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[]
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[][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen
ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or
[34]
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@textrm ([][]@texttt https:// cmake. org/ cmake/ help/ latest/ manual/ c
make-env-variables. 7. html#
[35]
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[]@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin
/cmake; fi[]
[36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
[51] [52] [53]
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[] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB
ILITY)" \[]
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[]@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX
PICFLAGS`[]
[54] [55] [56] [57] [58]
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[]@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19
20 21)[]
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[]@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[]
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[] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse
= "."))[]
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[] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[]
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[]@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor
version 52.0[]
[59]
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@texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b
e looked for
[60] [61] [62] [63] [64]
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@texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc.
gnu. org/ onlinedocs/ gcc/
[65] [66] [67]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[68]
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[][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0
/ rc2/ tools/ clang/ docs/ ReleaseNotes. html#
[69] [70] [71] [72] [73]
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[]@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro
ject. org[]@textrm )[][]) and RForge
Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[87]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4
[99] [100] [101] [102] [103] [104]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[105] [106] [107]
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@textrm See [][]@texttt https:// clang. llvm. org/ docs/ UsersManual. htm
l# controlling-code-generation[][][]@textrm ,
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[][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/
LightningTalks/ EuroLLVM%202014%20--%20container%20overflow.
[108]
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[]@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[]
[109]
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[110] [111]
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[]@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[]
[112] [113] [114] [115]
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[][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t
runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm :
[116]
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on [-Wlto-type-mismatch][]
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[]@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla
ration [-Wlto-type-mismatch][]
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[]@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar
ation [-Wlto-type-mismatch][]
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[]@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to
INTEGER(4)[]
Chapter 5 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126]
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[]
[127] [128] [129] [130] [131] [132] [133]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[134] [135] [136] [137] [138] [139] [140] [141] [142] [143]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155]
[156]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[157]
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[]
[158] Chapter 6 [159] [160] [161] [162] [163] [164] [165]
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[]@textrm Passing a variable-length string from C to For-tran is trick-ier, but
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[][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d
ocumentation/
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@texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere
nce/
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@texttt mixed-language-programming/ standard-tools-for-interoperability/ bind
. html[][][]
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175]
Warning: unbalanced parentheses in @def... [176] [177] [178] [179] [180]
[181]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [182] [183] Chapter 8 [184] [185] [186]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[187]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[188] [189] [190] [191] [192] [193]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[194] [195]
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[]@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [196]
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.vrs [197] [198] [199] [200])
(Concept index) [201] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.cps
[202]) [203] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
s/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texmf-dist/fonts/type1/public/
amsfonts/cm/cmbx12.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cm
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ist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texmf-dist/fonts/type1
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s/cm/cmr10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb><
/usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texmf
-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texmf-dist/fonts/type
1/public/amsfonts/cm/cmsl10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmsltt10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmss1
0.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texmf-dist/
fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmti9.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/c
m/cmtt10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb><
/usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texm
f-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb>
Output written on R-exts.pdf (209 pages, 1034529 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex)
restricted \write18 enabled.
entering extended mode
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(/usr/share/texmf-dist/tex/texinfo/texinfo.tex
Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings,
tables, conditionals, indexing, sectioning, toc, environments, defuns, macros,
cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-exts.vr
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi
(/usr/share/texmf-dist/tex/texinfo/txi-en.tex))
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f
onts/map/pdftex/updmap/pdftex.map}] [2]
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4]
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc)
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (Acknowledgements)
(/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.aux) Chapter 1 [1]
Writing index file R-exts.cp
[2] [3] [4] [5]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
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[] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec"
, "--no-test-load")[]
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[] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL
, quiet = TRUE)[]
[18]
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@texttt sourceforge. net/ projects/ tktable/ files/ tktable/ 2. 10/ Tkt
able2. 10. tar. gz[][][]@textrm , but
[19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29]
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[]@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[]
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[]@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[]
[30] [31] [32]
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[][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org
/ std/ standing-documents/
[33]
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[] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[]
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[][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen
ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or
[34]
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@textrm ([][]@texttt https:// cmake. org/ cmake/ help/ latest/ manual/ c
make-env-variables. 7. html#
[35]
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[]@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin
/cmake; fi[]
[36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
[51] [52] [53]
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[] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB
ILITY)" \[]
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[]@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX
PICFLAGS`[]
[54] [55] [56] [57] [58]
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[]@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19
20 21)[]
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[]@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[]
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[] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse
= "."))[]
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[] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[]
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[]@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor
version 52.0[]
[59]
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@texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b
e looked for
[60] [61] [62] [63] [64]
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@texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc.
gnu. org/ onlinedocs/ gcc/
[65] [66] [67]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[68]
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[][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0
/ rc2/ tools/ clang/ docs/ ReleaseNotes. html#
[69] [70] [71] [72] [73]
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[]@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro
ject. org[]@textrm )[][]) and RForge
Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[87]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4
[99] [100] [101] [102] [103] [104]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[105] [106] [107]
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@textrm See [][]@texttt https:// clang. llvm. org/ docs/ UsersManual. htm
l# controlling-code-generation[][][]@textrm ,
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[][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/
LightningTalks/ EuroLLVM%202014%20--%20container%20overflow.
[108]
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[]@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[]
[109]
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[110] [111]
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[]@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[]
[112] [113] [114] [115]
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[][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t
runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm :
[116]
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[]@texttt boot.f:61: warning: type of 'ddot' does not match original declarati
on [-Wlto-type-mismatch][]
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[]@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla
ration [-Wlto-type-mismatch][]
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[]@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar
ation [-Wlto-type-mismatch][]
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[]@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to
INTEGER(4)[]
Chapter 5 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126]
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[]
[127] [128] [129] [130] [131] [132] [133]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[134] [135] [136] [137] [138] [139] [140] [141] [142] [143]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155]
[156]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[157]
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[]
[158] Chapter 6 [159] [160] [161] [162] [163] [164] [165]
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[]@textrm Passing a variable-length string from C to For-tran is trick-ier, but
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[][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d
ocumentation/
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@texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere
nce/
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@texttt mixed-language-programming/ standard-tools-for-interoperability/ bind
. html[][][]
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175]
Warning: unbalanced parentheses in @def... [176] [177] [178] [179] [180]
[181]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [182] [183] Chapter 8 [184] [185] [186]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[187]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
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[]@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
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[]\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 []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/
n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth
-er-wise, it is []\T1/pcr/m/n/10 (double.base ^
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[]\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 . It
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\T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T
1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base
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[]\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, it is []\T1/pcr/m/n/10 (double.base
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\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p
cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As
[5]
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[]\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p
tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel
y anal-o-gously to their
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[][][]\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-l
ar,
[8] [9] [10]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
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[]\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v
alue = TRUE)[]
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[]\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i
gnore.case = TRUE)[]
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[]\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9)
# "absolute"[]
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[]\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean
rel.diff.=",[]
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
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[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
than 256 (or
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[]\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[]
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[]\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is
true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which
an
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[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
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[] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo
ne1970.tab"),[]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n
/10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2,
lwd = 1, bty="n")[]
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[]\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
"", type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
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\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 o
r
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
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[]\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
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[]\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 []\T1/pcr/m/n/10 c("first",
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[]\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 : / /
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\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}[]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n
/10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\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
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[]\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
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
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[]\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de
fault", "internal",
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[]\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri
ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n
/10 only. This
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\T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http
s : / / specifications . freedesktop .
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[]\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion
as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys-
[107] [108]
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[111] [112] [113] [114]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[115] [116] [117]
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/pcr/m/n/9 ## curlGetHeaders("ftp://cran.r-project.org") ## ftp::// suppo
rt is vanishing[]
[118] [119] [120] [121]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[122]
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[]\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
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[][][]\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
[123] [124] [125]
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[] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[]
[126] [127] [128] [129]
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\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 , and
[130] [131] [132] [133] [134] [135]
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[]\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions.
Func-tions should be listed in
[136] [137]
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[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
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[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[138] [139]
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[]\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha
racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b
y
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m
/n/10 formula[][][][]\T1/ptm/m/n/10 s, with
[140] [141] [142]
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[]\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
[143] [144] [145] [146] [147] [148] [149] [150] [151]
Underfull \hbox (badness 1917) in paragraph at lines 10410--10415
[]\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10
dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[152]
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[153] [154]
Underfull \hbox (badness 1168) in paragraph at lines 10568--10573
[]\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\
T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by
[155]
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[]\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n
ames(list(...));[]
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[]\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()),
names(list(...))))[]
[156] [157]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / /
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[158]
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[]\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[]
[159] [160]
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[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[161] [162] [163]
Underfull \hbox (badness 6396) in paragraph at lines 11242--11250
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
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[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len
t to but faster than
[164] [165] [166]
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[]\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D
LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use
[167] [168] [169] [170] [171] [172]
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[]\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma
y lead to con-fu-sion (see
[173]
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[]\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[]
[174] [175] [176]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1
0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt
m/m/n/10 and
[177]
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[]\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used
by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[178] [179] [180] [181]
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc
r/m/n/10 where []\T1/ptm/m/n/10 as
Underfull \hbox (badness 5970) in paragraph at lines 12557--12559
[]\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/10 is true, oth-er-wise
[182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193]
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[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[194] [195] [196] [197] [198] [199] [200] [201] [202] [203]
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[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
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[]\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m
a-tion is given about the
[204] [205]
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[]\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
[]\T1/pcr/m/n/10 fsep =
[206] [207]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[208] [209]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][][]\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 ,
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[][][]$\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 .
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[] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B
as it exists already[]
[210]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[211]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.exists[][][][]\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 ,
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[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[212]
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[]\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d
i-tion ob-ject of class
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[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
[213]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
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[]\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,
[214] [215] [216]
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[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
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[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[217] [218] [219] [220]
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[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
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[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
[221]
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[]\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-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[222]
Underfull \hbox (badness 6944) in paragraph at lines 15449--15452
[][][]\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/1
0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 ,
[223]
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[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[224] [225]
Underfull \hbox (badness 10000) in paragraph at lines 15612--15614
[]\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p
os-si-bly for-mat-ted) num-bers, also in
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[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
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[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[]
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[]\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
[226]
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[]\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
[227]
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[]\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 ,
which calls []\T1/pcr/m/n/10 .format.zeros(*,
Underfull \hbox (badness 10000) in paragraph at lines 15773--15778
[]\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call
s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri
des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10
formatC(123.45, mode =
Underfull \hbox (badness 10000) in paragraph at lines 15790--15798
[]\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
[228] [229]
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[]\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 ")[]
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[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
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[231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16754--16754
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[242] [243]
Underfull \hbox (badness 2418) in paragraph at lines 16863--16867
\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/pt
m/m/n/10 ,
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s
ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR
UE[]\T1/ptm/m/n/10 , then the sin-gle
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[][][]\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[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][]
\T1/ptm/m/n/10 ,
[244] [245]
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[]\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/
ptm/m/n/10 calls C level
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[]\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose
of flush-ing (i.e., emp-ty-ing) the
[246]
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[]\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f
actory" default[]
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[]\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if
translation works)[]
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[]\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex
ample started:[]
[248] [249]
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[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[250] [251] [252] [253]
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[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
[254]
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[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
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[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
[256] [257] [258] [259]
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[]\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)))
[260]
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[]\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[]
[261] [262] [263]
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[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[264] [265] [266] [267] [268]
Underfull \hbox (badness 1163) in paragraph at lines 18653--18655
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 https : / / unicode-[]org . github . io / icu /
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[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
[269]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[270]
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[] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se
t = FALSE,[]
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[] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F
ALSE,[]
[271]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
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[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
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[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
[272] [273]
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[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
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[]\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[]
[274] [275] [276]
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[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T
1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and
[277] [278] [279] [280] [281]
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[282] [283] [284]
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[]\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty
pes ([]\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 ,
[285] [286]
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[287] [288] [289]
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[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[290]
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[]\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co
lumn names differ)[]
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[]\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are
not checked)[]
[291] [292] [293] [294] [295] [296] [297] [298] [299]
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[]\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
[300] [301] [302] [303] [304] [305]
Underfull \hbox (badness 1077) in paragraph at lines 21124--21129
[]\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st
al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T
1/ptm/m/n/10 and
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[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
[306]
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[]\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the
en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 ,
[307]
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[]\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us
ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a
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\T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It
may be opened by
[308] [309]
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[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi
s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no
[]\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m
/n/10 ar-gu-ment, it lists all avail-able pack-
[310] [311]
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[][][]\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 autoloa
d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/
m/n/10 ,
[312]
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[]\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
[313]
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
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\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
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\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 21712--21717
\T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s
ion 3 of the li-cense can be dis-played by
[314] [315] [316]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[317]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/
m/n/10 for many more file han-dling func-tions and
[318] [319]
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[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
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[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
prob = 0.2))),[]
[320] [321]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
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[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
[322] [323]
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[]\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
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[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
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[]\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war
ning messages[]
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[] \T1/pcr/m/n/9 sg <- matrix(unlist(strsplit(strsplit(Sys.getlocale(), sep)[[
1]], "=")), nrow=2)[]
[324] [325]
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[][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[]
[][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m
/n/10 double[][][] []\T1/ptm/m/n/10 (class
[326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337]
[338]
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[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
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[] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N
aN, imaginary = r ))[]
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[]\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)[]
[339]
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[]\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE
) # |--> "abc"[]
[340]
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[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[341] [342] [343]
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[]\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 tcross
prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able.
[344] [345] [346] [347] [348] [349] [350] [351] [352]
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[]\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
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\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[353] [354]
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[355] [356] [357] [358] [359] [360] [361] [362]
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[]\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a
s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive =
[363]
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[]\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-
nally to a char-ac-ter vec-tor (so meth-ods for
[364]
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[]\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-r
e-spond-ing list,
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\T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\
T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env,
Underfull \hbox (badness 3148) in paragraph at lines 25206--25212
\T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi
-ron-ment is used as a hash ta-ble,
[365] [366] [367]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1
0 c("bytes", "chars",
[368] [369] [370]
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[]\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e
ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by
[371] [372] [373]
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\T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10
and in case of an er-ror (such as in-suf-fi-cient per-
[374] [375] [376] [377]
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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[]\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti
al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use
[378]
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[]\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m
ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab
out the pack-
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\T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c
om-puted pack-age in-for-ma-tion ob-ject and pass this to
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[]\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only)
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
[379]
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[]\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space
it loads to the search path.
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[]\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram
e con-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but
more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in%
[380]
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[] \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:[]
[381] [382] [383]
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[]\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
[][]mode[][][]
[384] [385] [386]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[387] [388] [389] [390]
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[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[391] [392]
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[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-
[393] [394]
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[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[395] [396]
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[398]
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[]\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 27629--27635
\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 27629--27635
\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 27642--27645
[]\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/pt
m/m/n/10 and
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[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 (and in-di-rectly
[399]
Underfull \hbox (badness 1009) in paragraph at lines 27728--27731
[]\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p
ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T
1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN
ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27752--27758
\T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1
/pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27752--27758
\T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5091) in paragraph at lines 27752--27758
[]\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma
c.binary.universal" []\T1/ptm/m/n/10 are no longer
Underfull \hbox (badness 10000) in paragraph at lines 27767--27774
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][][]\T1/pcr/m/n/10 up
date.packages[][][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 2384) in paragraph at lines 27767--27774
[]\T1/pcr/m/n/10 c(CRAN="@CRAN@")[]\T1/ptm/m/n/10 , a value that causes some ut
il-i-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 27767--27774
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke []\T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 27767--27774
\T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran";
[400] [401] [402] [403] [404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28115--28115
[]\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
300X faster[]
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[]\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.
y)] = FUN(X[arrayindex.x],
[405] [406]
Underfull \hbox (badness 1210) in paragraph at lines 28275--28278
[]\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la
ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex
t=s,
[407] [408] [409] [410]
Underfull \hbox (badness 7133) in paragraph at lines 28557--28563
[][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc
r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28579--28579
[]\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 28591--28591
[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
[411]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 28604--28604
[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling :
[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[]
[412] [413]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28791--28791
[]\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt
cars, cyl == 4))[]
[414]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28806--28806
[]\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so
is not evaluated[]
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[]\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., []\T1/pcr/m/n/10 type =
[415] [416] [417] [418] [419]
Underfull \hbox (badness 2277) in paragraph at lines 29173--29178
\T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt
m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing
[420] [421]
Underfull \hbox (badness 1701) in paragraph at lines 29289--29293
[]\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/
pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\
T1/pcr/m/n/10 get[][][](name, envir =
[422]
Underfull \hbox (badness 1796) in paragraph at lines 29357--29360
[]\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i
n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed
out-put, see
[423] [424] [425]
Underfull \hbox (badness 10000) in paragraph at lines 29561--29564
[]\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p
rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[426] [427] [428] [429] [430] [431] [432] [433] [434] [435]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 30256--30256
[] \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))[]
[436] [437] [438] [439] [440]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30549--30549
[]\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 30560--30560
[]\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 30566--30566
[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
[441]
Underfull \hbox (badness 7415) in paragraph at lines 30662--30666
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v
ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
[442]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 30683--30683
[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 30729--30729
[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
[443] [444]
Underfull \hbox (badness 3713) in paragraph at lines 30874--30885
[]\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma
n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm
/m/n/10 (not
[445] [446]
Underfull \hbox (badness 1248) in paragraph at lines 31026--31033
\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 31026--31033
\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 /
[447]
Underfull \hbox (badness 1533) in paragraph at lines 31144--31147
[]\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
[448] [449] [450]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 31289--31289
[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
Underfull \hbox (badness 1038) in paragraph at lines 31307--31318
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N
A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[451] [452]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31451--31451
[]\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[]
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[]\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
of deparse()[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31455--31455
[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31456--31456
[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h
ow = "unlist")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31463--31463
[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
[453] [454] [455] [456] [457]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 31771--31771
[]\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl
e prec numbers :[]
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[]\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
# split one double[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31783--31783
[]\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31784--31784
[]\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x)
numToBits(x) , raw(64L))[]
Underfull \vbox (badness 10000) has occurred while \output is active [458]
[459]
Underfull \hbox (badness 4048) in paragraph at lines 31879--31884
[]\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 31879--31884
\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 31879--31884
\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 ,
[460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 2080) in paragraph at lines 32417--32427
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/
10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n
/10 (ver-sion num-ber, cur-rently 2 or 3),
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32451--32451
[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[468] [469] [470] [471] [472] [473] [474]
Underfull \hbox (badness 7558) in paragraph at lines 32971--32975
[]\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p
tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 32981--32983
[]\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
[475]
Underfull \hbox (badness 10000) in paragraph at lines 32992--32994
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / /
pubs . opengroup . org / onlinepubs /
Underfull \hbox (badness 1975) in paragraph at lines 32995--32999
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m
/n/10 https : / / www .
[476] [477] [478] [479] [480]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33366--33366
[]\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete
replications[]
[481]
Underfull \hbox (badness 10000) in paragraph at lines 33437--33441
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[482] [483] [484]
Underfull \hbox (badness 2302) in paragraph at lines 33663--33668
[]\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-
ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant
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\T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/
10 round(x, dig -
[485] [486]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33796--33796
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33806--33806
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
[487] [488] [489] [490] [491] [492] [493]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34254--34254
[] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob)
&& size <= n/2))[]
[494] [495] [496] [497] [498] [499] [500]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34691--34691
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[501]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length
1, it ap-plies to all fields; oth-er-wise, if
[502] [503]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 34981--34981
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[504] [505] [506] [507]
Underfull \hbox (badness 4752) in paragraph at lines 35241--35244
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/
m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 5563) in paragraph at lines 35245--35251
[]\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
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517]
Underfull \hbox (badness 10000) in paragraph at lines 35915--35926
[]\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a
p-pli-ca-tion as well as
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\T1/ptm/m/n/10 the shell. It may de-pend on the com-piler used: Mi-crosoft's ru
les for the C run-
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\T1/ptm/m/n/10 time are given at [][]$\T1/pcr/m/n/10 https : / / docs . microso
ft . com / en-[]us / cpp / c-[]language /
Underfull \hbox (badness 1635) in paragraph at lines 35915--35926
\T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][
]\T1/ptm/m/n/10 . It may de-pend on the
[518] [519] [520] [521] [522] [523] [524] [525]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 36455--36455
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[526] [527] [528]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36707--36707
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 36709--36709
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[529]
Underfull \hbox (badness 4954) in paragraph at lines 36752--36758
[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/
pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T
1/ptm/m/n/10 , see also
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[][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \
T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[530] [531]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36863--36863
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[532] [533] [534] [535] [536]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37206--37206
[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37221--37221
[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[537] [538] [539]
Underfull \hbox (badness 10000) in paragraph at lines 37446--37448
[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
[540] [541] [542]
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[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
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[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[543] [544] [545] [546] [547]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 38005--38005
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[548]
Underfull \hbox (badness 6110) in paragraph at lines 38101--38111
[]\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-at
e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 38101--38111
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
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\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert
a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 38101--38111
\T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages
on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 38101--38111
\T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as
an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ).
Us-ing
[549]
Underfull \hbox (badness 10000) in paragraph at lines 38157--38163
[]\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 38157--38163
\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,
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\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
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 38172--38179
\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 38172--38179
\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
[550]
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[]\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba
ckslashes in[]
[551] [552] [553]
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[]\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T
1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
[554] [555] [556] [557] [558] [559] [560]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 38955--38955
[]\T1/pcr/m/n/9 (fF <- format(.POSIXct(notF))) # was all NA, now the last is
still NA (not "NA")[]
[561] [562]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 39064--39064
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[563] [564] [565]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[566]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[567] [568] [569] [570] [571] [572] [573]
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[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
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[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
[574]
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[]\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 39859--39866
[]\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form
at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m
/n/10 ).
[575]
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[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[576] [577] [578] [579]
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[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[580] [581] [582]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 40389--40389
[]\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.
[583]
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[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
Underfull \hbox (badness 2293) in paragraph at lines 40457--40463
[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 40457--40463
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call.
Underfull \hbox (badness 4792) in paragraph at lines 40476--40481
[]\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10
this may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 40476--40481
[]\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
[584] [585] [586] [587]
Underfull \hbox (badness 10000) in paragraph at lines 40764--40768
[]\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent
s []\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
[588]
Underfull \hbox (badness 1584) in paragraph at lines 40779--40782
[]\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy
s.function []\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
[589] [590]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 40917--40917
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[591]
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[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used
[592] [593]
Underfull \hbox (badness 1082) in paragraph at lines 41143--41146
[]\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions
keep their source in-clud-ing com-ments, see
[594]
Underfull \hbox (badness 10000) in paragraph at lines 41170--41172
[][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo
adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li
brary[][][](.) []\T1/ptm/m/n/10 and uses
[595] [596]
Underfull \hbox (badness 1038) in paragraph at lines 41336--41339
[]\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c
at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[597] [598] [599] [600] [601]
Underfull \hbox (badness 1442) in paragraph at lines 41701--41705
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout
= TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout =
[602] [603] [604] [605]
Underfull \hbox (badness 4096) in paragraph at lines 41955--41958
[]\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri
nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin.
table[][][][]\T1/ptm/m/n/10 ,
[606]
Underfull \hbox (badness 7888) in paragraph at lines 42069--42073
[]\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can
have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/
m/n/10 length(bin) >
[607] [608] [609]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 42223--42223
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
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[] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[]
Overfull \hbox (55.67578pt too wide) in paragraph at lines 42227--42227
[] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 =
NULL), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 42240--42242
[]\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t
hat was reg-is-tered ear-lier via
[610]
Underfull \hbox (badness 10000) in paragraph at lines 42320--42323
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[611] [612]
Underfull \hbox (badness 3872) in paragraph at lines 42438--42441
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 5475) in paragraph at lines 42504--42508
[][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback
Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[614] [615] [616] [617] [618] [619]
Underfull \hbox (badness 1655) in paragraph at lines 42927--42934
\T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[]
\T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1
/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ',
Underfull \hbox (badness 2253) in paragraph at lines 42935--42940
[]\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se
e the ex-am-ples for typ-i-cal cases. It may
Underfull \hbox (badness 1655) in paragraph at lines 42935--42940
\T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 ,
some-thing like `[]\T1/pcr/m/n/10 "2020a"[]\T1/ptm/m/n/10 '. (It does on sys-te
ms us-ing
Underfull \hbox (badness 4467) in paragraph at lines 42985--42994
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-
turns the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 42985--42994
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
[620]
Underfull \hbox (badness 1082) in paragraph at lines 42995--43007
[]\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/1
0 ' in that di-rec-tory states the ver-sion. That op-tion is
[621]
Underfull \hbox (badness 1337) in paragraph at lines 43080--43088
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
Underfull \hbox (badness 3460) in paragraph at lines 43143--43146
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 43147--43149
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
[622]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 43156--43156
[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[623] [624] [625] [626]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 43499--43499
[]\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 43501--43501
[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
[627]
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Overfull \hbox (84.78088pt too wide) in paragraph at lines 43602--43602
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 43604--43604
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
[629] [630] [631] [632]
Underfull \hbox (badness 6542) in paragraph at lines 43878--43880
[]\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 , an
d
[633]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 43997--43997
[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
[634]
Underfull \hbox (badness 1708) in paragraph at lines 44065--44073
[]\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any
er-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 44065--44073
\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
[635]
Underfull \hbox (badness 4859) in paragraph at lines 44105--44110
[][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle
rs and sup-press-ing the print-ing of er-ror mes-sages;
[636]
Underfull \hbox (badness 3895) in paragraph at lines 44167--44179
[]\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 44167--44179
\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 ,
[637] [638] [639] [640] [641]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 44490--44490
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[642] [643] [644] [645] [646] [647]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44959--44959
[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
[648]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 44968--44968
[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[]
Underfull \hbox (badness 2057) in paragraph at lines 45034--45040
[][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc
ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n
/10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][]
\T1/ptm/m/n/10 ,
[649]
Underfull \hbox (badness 3861) in paragraph at lines 45043--45048
[][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di
r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/
ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\
T1/ptm/m/n/10 ,
[650]
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[]\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[]
[651]
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[]\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\
T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ),
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[]\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
[652] [653] [654]
Underfull \hbox (badness 3668) in paragraph at lines 45432--45434
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[655]
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[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[656] [657]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 45613--45613
[]\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[]
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[]\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
There were 105 warnings ...[]
[658]
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[]\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[]
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[]\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings
AsFactors = FALSE) {[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 45720--45720
[] \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa
ctors=stringsAsFactors)[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix
- dropping time info {sec,min,hour, isdst}[]
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[]\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[]
[659]
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[]\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
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[]\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name
ly a ma-trix whose rows each
[660] [661]
Underfull \hbox (badness 2818) in paragraph at lines 45887--45893
[]\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 and []\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
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[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[662] [663] [664] [665] [666] [667] [668]
Underfull \hbox (badness 2846) in paragraph at lines 46381--46385
[]\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren
tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[669]
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[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
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[]\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da
rd' reg-exps, in-clud-ing el-e-ments named
[670]) (./compiler-pkg.tex
Chapter 2.
[671]
Underfull \hbox (badness 2884) in paragraph at lines 106--120
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b
e used to con-trol com-piler op-er-a-tion. There are cur-
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\T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef
ined[]\T1/ptm/m/n/10 , and
[672] [673] [674]) (./datasets-pkg.tex
Chapter 3.
[675] [676] [677] [678] [679]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301
[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[680]
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[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
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[682] [683] [684]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617
[] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[]
[685]
Underfull \hbox (badness 4779) in paragraph at lines 704--707
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[686] [687]
Underfull \hbox (badness 4779) in paragraph at lines 837--840
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[688] [689] [690]
Underfull \hbox (badness 1097) in paragraph at lines 1037--1041
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[691]
Underfull \hbox (badness 4779) in paragraph at lines 1152--1155
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[692] [693] [694] [695] [696]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464
[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[697] [698]
Underfull \hbox (badness 10000) in paragraph at lines 1549--1552
[]\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr
ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q
uarterly.revenue[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1549--1552
[]\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-taine
d from the above
[699] [700] [701]
Underfull \hbox (badness 4779) in paragraph at lines 1738--1741
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[702]
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[]\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 1840--1840
[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[703] [704]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956
[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957
[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[705] [706] [707] [708]
Underfull \hbox (badness 4779) in paragraph at lines 2160--2163
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[709] [710] [711]
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[712] [713] [714] [715] [716]
Underfull \hbox (badness 4779) in paragraph at lines 2725--2728
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[717]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[718]
Underfull \vbox (badness 2376) has occurred while \output is active [719]
[720] [721] [722] [723]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154
[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[724] [725] [726] [727] [728] [729] [730] [731]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3611--3611
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[732] [733]
Underfull \hbox (badness 4779) in paragraph at lines 3759--3762
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[734]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[735]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[736]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3968--3968
[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
Underfull \hbox (badness 10000) in paragraph at lines 4006--4008
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
Underfull \hbox (badness 10000) in paragraph at lines 4006--4008
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750]) (./grDevices-pkg.tex
Chapter 4.
[751] [752] [753] [754]
Underfull \hbox (badness 4752) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/
ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p
tm/m/n/10 in
[755] [756] [757] [758]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[759] [760] [761] [762] [763] [764] [765] [766] [767] [768]
Underfull \hbox (badness 5175) in paragraph at lines 1192--1194
[]\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
[769] [770] [771]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363
[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[772] [773] [774]
Underfull \hbox (badness 3302) in paragraph at lines 1624--1628
[]\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo
re of
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[]\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern")
[775] [776] [777] [778] [779]
Underfull \hbox (badness 1565) in paragraph at lines 1914--1919
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i
s to pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1914--1919
\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
[780]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[781]
Underfull \hbox (badness 1184) in paragraph at lines 2038--2048
[]\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 2038--2048
[]\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp
ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 ,
[782]
Underfull \hbox (badness 10000) in paragraph at lines 2150--2152
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[783] [784] [785]
Underfull \hbox (badness 6758) in paragraph at lines 2329--2332
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[786] [787]
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[]\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se
tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place
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\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
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\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 2447--2457
[]\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10
setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics
[788]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[789] [790]
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[]\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2667--2667
[]\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[]
[791] [792] [793] [794]
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[796] [797] [798] [799]
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[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[800]
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[]\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 3358--3358
[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[801] [802] [803]
Underfull \hbox (badness 10000) in paragraph at lines 3516--3522
[]\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b
ased on the inter-quartile range
[804]
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[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[]
[805]
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[]\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[]
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[]\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[]
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[] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab =
"", main=main)[]
[806]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
[807]
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[]\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 ,
[808]
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[]\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work
s well for shad-ing points or lines in up to five groups,
Underfull \hbox (badness 10000) in paragraph at lines 3886--3890
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[809]
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Underfull \hbox (badness 5260) in paragraph at lines 4016--4019
[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10
give a C in-te-ger for-mat such as
[811] [812] [813] [814] [815]
Underfull \hbox (badness 5939) in paragraph at lines 4349--4354
[]\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 family[]\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 ,
[816] [817] [818] [819] [820] [821] [822] [823]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4869--4869
[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[824] [825]
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[826]
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
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[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10
give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as
[827]
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[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), []\T1/pcr/m/n/10 "CP1251.enc"
[828]
Underfull \hbox (badness 1755) in paragraph at lines 5314--5316
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[829] [830] [831]
Underfull \hbox (badness 7344) in paragraph at lines 5494--5496
[]\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 5505--5509
[][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][]
[]\T1/ptm/m/n/10 which is called from both
[832] [833]
Underfull \hbox (badness 1552) in paragraph at lines 5632--5641
[]\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 "He
lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10
,
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal
atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc
r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\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/p
cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2221) in paragraph at lines 5642--5644
[]\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and
Underfull \hbox (badness 4686) in paragraph at lines 5674--5680
[]\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p
cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for
[834]
Underfull \hbox (badness 5388) in paragraph at lines 5700--5702
[]\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p
cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
[835] [836]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803
[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[837]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5915--5915
[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
[838] [839]
Underfull \hbox (badness 10000) in paragraph at lines 6001--6003
[]\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][]
\T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T
1/ptm/m/n/10 for on-screen de-vices and to
[840] [841] [842] [843] [844]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6368--6368
[]\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 6382--6385
[]\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r
ed/green/blue) into HSV space
[845] [846] [847] [848] [849] [850]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6717--6717
[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6724--6724
[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
[851] [852] [853] [854]
Underfull \hbox (badness 10000) in paragraph at lines 6990--6995
[]\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 pointsize[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10
,
Underfull \hbox (badness 1803) in paragraph at lines 6990--6995
[]\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/
ptm/m/n/10 ,
Underfull \hbox (badness 2941) in paragraph at lines 6990--6995
[]\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi
rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
fillOddEven []\T1/ptm/m/n/10 and
[855]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7096--7096
[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
[856]
Underfull \hbox (badness 3590) in paragraph at lines 7135--7138
[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 2393) in paragraph at lines 7135--7138
\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7146--7146
[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
[857]
Underfull \hbox (badness 1189) in paragraph at lines 7211--7213
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[858]
Underfull \hbox (badness 10000) in paragraph at lines 7316--7318
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ
K lan-guages and
[859]
Underfull \hbox (badness 10000) in paragraph at lines 7362--7369
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of []
\T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2469) in paragraph at lines 7362--7369
[]\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu
x sys-tems which have the Wine
[860]
Underfull \hbox (badness 5607) in paragraph at lines 7446--7450
[]\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d
o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and
[861]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7498--7498
[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[862] [863]
Underfull \hbox (badness 5637) in paragraph at lines 7630--7636
[]\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 7663--7666
[]\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 /
[864] [865] [866]
Underfull \hbox (badness 1231) in paragraph at lines 7832--7834
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10
number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of
[867] [868]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 4647) 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 []\T1/pcr/m/n/10 library(help =
[869] [870] [871] [872] [873] [874] [875]
Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450
[] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[]
Underfull \hbox (badness 4048) in paragraph at lines 482--488
[]\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
[876] [877]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580
[]\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[]
[878]
Underfull \hbox (badness 10000) in paragraph at lines 694--698
[]\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 694--698
[][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T
1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\
T1/ptm/m/n/10 if
[879] [880]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 770--770
[]\T1/pcr/m/n/9 ## 1e-01 1e+01 1e+03 1e+05 1e+07 1e+09 1e+11 ; since R 4.2.0:
1e-2 1e0 1e2 .. 1e10[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 782--782
[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 819--819
[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
[881] [882] [883]
Underfull \hbox (badness 10000) in paragraph at lines 966--970
[][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1
/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl
e.
Overfull \hbox (133.98029pt too wide) in paragraph at lines 983--983
[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 985--985
[]\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset
= Age=="Adult"))[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 987--987
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
[884] [885] [886] [887]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1271--1271
[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
[888] [889] [890]
Underfull \hbox (badness 2503) in paragraph at lines 1433--1442
\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and
[]\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3375) in paragraph at lines 1468--1470
[]\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt
m/m/n/10 ),
[891] [892]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1542--1542
[]\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 1543--1543
[]\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 1549--1549
[]\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 1550--1550
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[893] [894] [895] [896] [897]
Underfull \hbox (badness 10000) in paragraph at lines 1853--1859
[][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr
/m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1873--1873
[]\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1885--1885
[]\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1901--1901
[]\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 1910--1910
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
[898] [899]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1995--1995
[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[900] [901]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2124--2124
[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2129--2129
[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
[902] [903]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2303--2303
[]\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 2304--2304
[] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[]
[904]
Underfull \hbox (badness 1430) in paragraph at lines 2335--2337
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10
"n" []\T1/ptm/m/n/10 to sup-press and see also
[905]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2416--2416
[] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[]
Underfull \hbox (badness 1009) in paragraph at lines 2428--2435
\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
[906]
Underfull \hbox (badness 7273) in paragraph at lines 2510--2514
[][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p
tm/m/n/10 and
[907] [908] [909] [910]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2758--2758
[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[911]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2795--2795
[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[912] [913]
Underfull \hbox (badness 1226) in paragraph at lines 2923--2927
\T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1
/pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy
[914]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2976--2976
[]\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 2980--2980
[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[915]
Underfull \hbox (badness 10000) in paragraph at lines 3042--3045
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1
/pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3093--3093
[]\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w
rong" message:[]
[916] [917] [918]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3257--3257
[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3262--3262
[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[919] [920]
Underfull \hbox (badness 10000) in paragraph at lines 3404--3409
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f
ied, raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3404--3409
[][][]\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 3404--3409
[][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt
m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is
[921] [922] [923]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3590--3590
[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3609--3609
[] \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 3613--3613
[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[924] [925] [926]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3798--3798
[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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[] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l
engths & coords[]
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[] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
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[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc
r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[]
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[]\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow
(VADeaths)))[]
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[]\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7
, lty = 1:7,[]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
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[]\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset
= .02",inset = .02)[]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
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[]\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized"
, "columns."),[]
[929]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth
od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\
T1/pcr/m/n/10 type %in%
[930]
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[931] [932] [933]
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[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
[934]
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[]\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
[935] [936] [937] [938] [939]
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[]\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
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[]\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
[940] [941]
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor,[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
[942]
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\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/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 axis[][][][]\T1/ptm/m/n/10 ,
[943] [944] [945] [946]
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[947 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//mai.pdf>]
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[948 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//oma.pdf>]
[949] [950]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[952] [953] [954] [955] [956]
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[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
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[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
[957]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again>
\relax
l.5943 \aliasA{plot}{plot.default}{plot}
[958] [959] [960] [961] [962]
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[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[963] [964]
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[] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co
llapse = "\n")),[]
[965] [966] [967] [968]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[969] [970]
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[]\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
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[][]
[971 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//pch.pdf>]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
[972]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[974]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[975]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T
1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or
[976] [977] [978] [979]
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[980] [981] [982] [983] [984] [985]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
[986]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[987] [988] [989] [990] [991]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[992] [993] [994]
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[]\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)
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[]\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)[]
[995] [996]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
[997]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh
tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 )
is drawn. For
[998]
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[]
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
lambda = 2),[]
[999] [1000]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[1001] [1002]
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[] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile:
Règles, Liberté, Egalité, Fraternité...")[]
[1003]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m
/n/10 par(c("font.sub",
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[]\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 a
re []\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
[1004]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
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\relax
l.9018 \HeaderA{units}{Graphical Units}{units}
[1005]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[1006] [1007]
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[]\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)[]
[1008]) (./grid-pkg.tex
Chapter 6.
[1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018]
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
to the
[1019] [1020] [1021] [1022] [1023] [1024]
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
[1025] [1026] [1027]
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[] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
[1028] [1029] [1030] [1031]
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[]\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
[1032] [1033] [1034] [1035] [1036] [1037] [1038]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[1039] [1040] [1041]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[]
[1042]
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[]\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 ,
[1043]
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[]\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
[1044] [1045] [1046]
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[]\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
[1047] [1048] [1049]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
[1050]
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
[1051] [1052]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
[1053]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[1054] [1055]
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[]\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix;
see
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1064] [1065]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just=
c("left", "bottom")))[]
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[]\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa
ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see
[1066] [1067]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
[1068] [1069] [1070]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
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[]\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[]
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[1083]
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[]\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
[1084] [1085] [1086] [1087]
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
[1088] [1089]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve
c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list
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\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For
[]\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther
[1096] [1097]
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[]\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob
-ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a
[1098] [1099] [1100]
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a
r-gu-ments above are passed to
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[1112] [1113] [1114] [1115] [1116] [1117]
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
[1118]
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[]\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip()
, device=TRUE)
[1119] [1120]
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[]\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
[1121]
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[][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push
Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 ,
[1122] [1123] [1124] [1125] [1126]
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
[1127]) (./methods-pkg.tex [1128]
Chapter 7.
[1129] [1130]
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[]\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how
co-erce meth-ods work. Use
[1131] [1132] [1133]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in-
for-ma-tion about group generic func-tions; [][]Meth-
[1134] [1135]
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[]\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall
y a primitive.[]
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[]\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[]
[1136]
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[]\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[]
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[]\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[]
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[]\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b
y callNextMethod[]
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[]\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
"B0" method[]
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[]\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[
]
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[1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
[1150] [1151] [1152]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
[1153] [1154]
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[]\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/
10 can be an ob-ject of class
[1155] [1156] [1157]
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[]\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 =
[1158] [1159]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment
[][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
[1160] [1161] [1162]
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[]\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\
T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c
re-ate ob-jects of class
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[]\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
[1163]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1164] [1165] [1166]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1167] [1168] [1169] [1170] [1171] [1172] [1173]
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[]\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r
e-turns the im-plicit generic ver-sion,
Underfull \hbox (badness 6268) in paragraph at lines 3402--3407
[]\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici
t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents
[1174] [1175]
Underfull \hbox (badness 10000) in paragraph at lines 3530--3534
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10
getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class
[1176]
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[]
[1177] [1178]
Underfull \hbox (badness 10000) in paragraph at lines 3761--3762
[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit
ude =
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
[1179]
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,
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[]\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
[1180] [1181] [1182] [1183] [1184] [1185]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312
[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
[1186]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1187] [1188] [1189]
Underfull \hbox (badness 2126) in paragraph at lines 4578--4586
[]\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 ,
[1190] [1191] [1192]
Underfull \hbox (badness 10000) in paragraph at lines 4815--4824
[]\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
[1193] [1194] [1195] [1196]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5203--5203
[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1197]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[1199]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1200] [1201]
Underfull \hbox (badness 3803) in paragraph at lines 5520--5522
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1202] [1203] [1204]
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[]\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
[1205] [1206] [1207] [1208] [1209] [1210]
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p
tm/m/n/10 is equiv-a-lent to in-vok-ing the method
[1211] [1212]
Underfull \hbox (badness 1248) in paragraph at lines 6351--6355
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T
1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions,
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\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
[1213]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1214] [1215]
Underfull \hbox (badness 2875) in paragraph at lines 6655--6664
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][][]\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
[1216]
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[1218] [1219]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6981 \aliasA{S4}{S3Part}{S4}
[1220]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
[1221] [1222]
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[]\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
datasets::iris)[]
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[]\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[]
[1223]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again>
\relax
l.7237 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
ignored
<to be read again>
\relax
l.7239 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again>
\relax
l.7240 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.7242 \aliasA{Ops}{S4groupGeneric}{Ops}
pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7243 \aliasA{Summary}{S4groupGeneric}{Summary}
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[]\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
[1224]
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[]\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p
tm/m/n/10 , []\T1/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 7317--7329
[]\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p
tm/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 "c
os"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp
i"[]\T1/ptm/m/n/10 ,
[1225] [1226]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
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[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS
uperClasses() []\T1/ptm/m/n/10 which calls
[1227]
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[]\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[]
[1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238]
[1239] [1240]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1241]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1242] [1243] [1244] [1245]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1246] [1247] [1248]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1249] [1250] [1251]
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[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
[1252] [1253] [1254] [1255]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1256]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
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[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi
on" []\T1/ptm/m/n/10 for class
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[]\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.,
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[]\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10
"function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1267] [1268] [1269]) (./parallel-pkg.tex [1270]
Chapter 8.
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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p
cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][]
RNG[][][]: see
[1271]
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[]\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a
nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for
[1272] [1273]
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[]\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
[1274]
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD,
So-laris and Win-dows.
[1275] [1276]
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[]\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
[1277] [1278] [1279] [1280] [1281]
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[]\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
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[]\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe
s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If
[1282] [1283]
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[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1284] [1285] [1286]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
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[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1287]
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[]\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
[1288]
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[]\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 1243--1243
[]\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)[]
[1289] [1290]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1359--1359
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
[1291]
Underfull \hbox (badness 1577) in paragraph at lines 1402--1405
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10
.Random.seed []\T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1449--1451
[]\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
[1292] [1293]) (./splines-pkg.tex [1294]
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 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1303]
Underfull \hbox (badness 1043) in paragraph at lines 597--599
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec
t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the
[1304] [1305]
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[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1306] [1307] [1308]) (./stats-pkg.tex
Chapter 10.
[1309]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\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"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
[]\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
Species" with 3 levels:[]
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[] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
list, as no factors[]
[1310] [1311] [1312] [1313] [1314]
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[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
[1315]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1316] [1317] [1318] [1319] [1320] [1321]
Underfull \hbox (badness 1024) in paragraph at lines 887--889
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l
m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for
[1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1625--1625
[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
[1333] [1334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1775--1775
[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
[1335]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1787--1787
[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
]
[1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346]
[1347] [1348] [1349]
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[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1350] [1351] [1352] [1353]
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[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1354] [1355] [1356]
Underfull \hbox (badness 10000) in paragraph at lines 3264--3266
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo
geneity of
[1357]
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[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1358] [1359] [1360] [1361]
Package amsmath Warning: Foreign command \atopwithdelims;
(amsmath) \frac or \genfrac should be used instead
(amsmath) on input line 3642.
[1362]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3708--3708
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1363] [1364] [1365] [1366]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3987--3987
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1367] [1368] [1369] [1370] [1371]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4276--4276
[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1372] [1373] [1374] [1375]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4518--4518
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1376] [1377]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4693--4693
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1378] [1379]
Underfull \hbox (badness 3989) in paragraph at lines 4787--4794
[]\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 =
[1380] [1381] [1382] [1383] [1384]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5172--5172
[]\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 5174--5174
[]\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))[]
[1385] [1386] [1387]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5396--5396
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
[1388] [1389] [1390] [1391]
Underfull \hbox (badness 1436) in paragraph at lines 5624--5629
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
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\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 5624--5629
\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 ,
[1392] [1393] [1394]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5827--5827
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1395] [1396]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5994--5994
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1397] [1398] [1399]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6179--6179
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1400] [1401]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6287--6287
[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
[1402] [1403] [1404] [1405]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1406]
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[]\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca
n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing
method
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[]\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g
ram []\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 6639--6644
\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,
[1407]
Underfull \hbox (badness 7238) in paragraph at lines 6675--6678
[][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti
on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend
rogram[][][] []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[]
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[]\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 6725--6725
[]\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):[]
[1408]
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[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
[1409] [1410] [1411]
Underfull \vbox (badness 10000) has occurred while \output is active [1412]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6994--6994
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1413] [1414]
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[1416] [1417] [1418]
Underfull \hbox (badness 10000) in paragraph at lines 7394--7398
[]\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 "bi
nary" []\T1/ptm/m/n/10 or
[1419]
Underfull \hbox (badness 6493) in paragraph at lines 7493--7496
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][]
\T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the
[1420] [1421]
Underfull \hbox (badness 10000) in paragraph at lines 7630--7633
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427]
Underfull \hbox (badness 10000) in paragraph at lines 8042--8047
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences []
\T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 ,
...,
[1428] [1429] [1430] [1431] [1432] [1433]
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[]\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al
so be sup-plied as named ar-gu-ments to
[1434] [1435] [1436] [1437] [1438] [1439]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8860--8860
[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
[1440]
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[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
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[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9488--9488
[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9489--9489
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
[1449] [1450] [1451]
Underfull \hbox (badness 7291) in paragraph at lines 9668--9670
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test
of homogeneity of
[1452] [1453] [1454] [1455] [1456] [1457] [1458]
Underfull \hbox (badness 6944) in paragraph at lines 10160--10166
[][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in-
ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment
);
[1459] [1460] [1461]
Underfull \hbox (badness 3758) in paragraph at lines 10374--10377
[]\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
[1462] [1463] [1464] [1465]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10618--10618
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
Underfull \hbox (badness 4518) in paragraph at lines 10644--10649
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1466]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
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[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second
[]\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 10788--10791
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic
ients[][][][]\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
[1468] [1469] [1470]
Underfull \hbox (badness 2142) in paragraph at lines 11005--11008
[]\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 ^^@
[1471]
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[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1472]
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[][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1
0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1
0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11166--11171
[]\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui
tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (=
[1473] [1474]
Underfull \hbox (badness 2635) in paragraph at lines 11299--11302
\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/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 )
meth-ods and the
[1475] [1476] [1477]
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1478]
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
[1479]
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[] \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 11626--11630
[]\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\
T1/ptm/m/n/10 (the de-fault) or
[1480] [1481] [1482] [1483] [1484]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11948--11948
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
[1485]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again>
\relax
l.11963 \aliasA{hat}{influence.measures}{hat}
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12023--12023
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
[1486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12035--12035
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
Underfull \hbox (badness 1062) in paragraph at lines 12088--12093
[]\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me
nts are there to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12105--12107
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists
mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1487] [1488] [1489] [1490]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12360--12360
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12361--12361
[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 10000) in paragraph at lines 12707--12709
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de
fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12730--12732
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 3417) in paragraph at lines 13037--13039
[]\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 []\T1/pcr/m/n/10 ob <-
Underfull \hbox (badness 2894) in paragraph at lines 13043--13047
[]\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 13043--13047
\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti
ve (or true), trac-ing in-for-ma-tion on the
[1502] [1503] [1504] [1505] [1506] [1507]
Underfull \hbox (badness 1496) in paragraph at lines 13457--13463
[]\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran-
dom-iza-tion Dis-tri-bu-tions of
[1508] [1509] [1510] [1511]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13706--13706
[]\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[]
[1512]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13807--13807
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1513]
Underfull \hbox (badness 4518) in paragraph at lines 13855--13860
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516]
Underfull \hbox (badness 10000) in paragraph at lines 14062--14066
[]\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava
il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][]
[]\T1/ptm/m/n/10 ,
[1517] [1518] [1519] [1520] [1521]
Underfull \hbox (badness 1163) in paragraph at lines 14402--14410
\T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc
on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re
siduals[][][][]\T1/ptm/m/n/10 ,
[1522] [1523]
Underfull \hbox (badness 4518) in paragraph at lines 14522--14527
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1524] [1525] [1526]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14710--14710
[]\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 14711--14711
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1527] [1528] [1529] [1530] [1531]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15054--15054
[]\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 15055--15055
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1532]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 15148--15148
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1533] [1534] [1535] [1536] [1537] [1538] [1539]
Underfull \hbox (badness 2726) in paragraph at lines 15557--15560
[]\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [
]\T1/pcr/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 ,
[1540]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15651--15651
[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
[1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 16278--16278
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1551] [1552]
Underfull \hbox (badness 1490) in paragraph at lines 16425--16430
\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
[1553]
Underfull \hbox (badness 1648) in paragraph at lines 16491--16493
[]\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,
[1554]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16576--16576
[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16577--16577
[]\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[]
[1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17134--17134
[]\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[]
[1564] [1565] [1566]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17366--17366
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576]
Underfull \vbox (badness 10000) has occurred while \output is active [1577]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 18088--18088
[]\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
Underfull \vbox (badness 10000) has occurred while \output is active [1578]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 18106--18106
[]\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n
umerical differentiation,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 18107--18107
[]\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo
w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 18111--18111
[]\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co
nverging on *some*):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18112--18112
[]\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal
ler than above[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 18115--18115
[] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl
("^NixOS", osVersion)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18147--18147
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1579] [1580] [1581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18323--18323
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
[1582]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18370--18370
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18417--18417
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1583] [1584] [1585] [1586]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 18623--18623
[] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[]
[1587] [1588] [1589] [1590] [1591]
Underfull \hbox (badness 1248) in paragraph at lines 18938--18941
[]\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 1661) in paragraph at lines 18951--18955
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18959--18963
\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
[1592]
Underfull \hbox (badness 2042) in paragraph at lines 19017--19019
[]\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
[1593]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 19123--19123
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
[1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19166--19166
[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19184--19184
[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19187--19187
[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19207--19207
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
[1595]
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[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
Underfull \hbox (badness 2564) in paragraph at lines 19245--19256
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva
l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m
/n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/
10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19245--19256
\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
[1596]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19308--19308
[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1597] [1598] [1599]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19535--19535
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1600] [1601]
Underfull \hbox (badness 1337) in paragraph at lines 19646--19649
[]\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
[1602] [1603] [1604] [1605] [1606]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19965--19965
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1607] [1608]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 20053--20053
[] \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 (12.78088pt too wide) in paragraph at lines 20055--20055
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20057--20057
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1609]
Underfull \hbox (badness 10000) in paragraph at lines 20117--20123
\T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di
stance", lty = cook.lty,
Underfull \hbox (badness 10000) in paragraph at lines 20117--20123
\T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp
Underfull \hbox (badness 10000) in paragraph at lines 20125--20131
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T
1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 20136--20139
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m
/n/10 ylim <-
[1610] [1611] [1612] [1613] [1614]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20437--20437
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 1194) in paragraph at lines 20447--20450
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1615]
Underfull \hbox (badness 1107) in paragraph at lines 20505--20507
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate []
\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to
[1616]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20560--20560
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20567--20567
[]\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)[]
[1617] [1618]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20661--20661
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1619] [1620]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20790--20790
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1621]
Underfull \hbox (badness 7740) in paragraph at lines 20853--20855
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [
]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20901--20901
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1622]
Underfull \hbox (badness 10000) in paragraph at lines 20957--20959
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 polym(*, coefs=<non-NULL>)[]\T1/ptm/m/n/10 , and
[1623]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20994--20994
[] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or
just poly():[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20999--20999
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634]
[1635] [1636]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 21854--21854
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[]
[1637]
Underfull \hbox (badness 6859) in paragraph at lines 21921--21928
[][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21932--21938
[]\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/1
0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 ,
[1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648]
[1649]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22678--22678
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1650] [1651] [1652] [1653] [1654]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22962--22962
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22963--22963
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1655] [1656] [1657] [1658] [1659]
Underfull \hbox (badness 1337) in paragraph at lines 23289--23295
[]\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
[1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667]
Underfull \hbox (badness 10000) in paragraph at lines 23848--23850
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 23848--23850
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 23855--23856
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
[1668] [1669]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 23966--23966
[] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[]
[1670]
Underfull \hbox (badness 1028) in paragraph at lines 24024--24027
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T
1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and
[1671] [1672]
Underfull \hbox (badness 10000) in paragraph at lines 24139--24142
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\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 [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1673]
Underfull \hbox (badness 7099) in paragraph at lines 24258--24260
[]\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 [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1674]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24293--24293
[]\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median,
decreasing=TRUE))[]
[1675]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24369--24369
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1676] [1677]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24486--24486
[]\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with
care)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24487--24487
[]\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long
format[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24488--24488
[]\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time
variable[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24489--24489
[]\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v
ariable[]
[1678] [1679]
Underfull \hbox (badness 10000) in paragraph at lines 24649--24654
[][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[]
[][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r
e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [
][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 24649--24654
[][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing
con-tin-gency ta-bles and con-vert-ing them back to
[1680]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24660--24660
[]\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24661--24661
[]\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24680--24680
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1681]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24784--24784
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
[1682]
Underfull \hbox (badness 1033) in paragraph at lines 24827--24833
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
Underfull \hbox (badness 10000) in paragraph at lines 24848--24851
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r
unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] =
[1683]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24930--24930
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1684]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24959--24959
[]\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
used to fail badly (notably for "Turlach"):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24971--24971
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
[1685] [1686] [1687] [1688] [1689] [1690] [1691]
Underfull \hbox (badness 6268) in paragraph at lines 25429--25434
[][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S
Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo
mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 ,
[1692] [1693] [1694] [1695]
Underfull \hbox (badness 1867) in paragraph at lines 25638--25640
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods.
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 25653--25657
[]\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba
ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25653--25657
\T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where
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 25689--25689
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25696--25696
[]\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[]
[1696] [1697] [1698]
Underfull \hbox (badness 2495) in paragraph at lines 25879--25888
[]\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 .
[1699] [1700]
Underfull \hbox (badness 2197) in paragraph at lines 26021--26024
[]\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion,
[]\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and
[1701]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 26041--26041
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
Underfull \hbox (badness 1412) in paragraph at lines 26048--26050
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1702]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26135--26135
[]\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 26160--26160
[]\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 26163--26163
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1703] [1704] [1705]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26392--26392
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 26396--26402
[]\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/
10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in
g only
[1706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26442--26442
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26463--26463
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1707] [1708] [1709]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26655--26655
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1710] [1711] [1712] [1713] [1714] [1715] [1716]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 27035--27035
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1717] [1718]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27216--27216
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 27222--27222
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))
for when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27231--27231
[]\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 27232--27232
[]\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 [1719]
Underfull \hbox (badness 2922) in paragraph at lines 27301--27306
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1720]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27338--27338
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27341--27341
[] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27350--27350
[] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27351--27351
[] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
# (Asym + R0)/2[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27355--27355
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1721]
Underfull \hbox (badness 3240) in paragraph at lines 27409--27412
[][][]\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 graph show-ing the []\T1/pcr/m/n/10 SSasympOff
[1722]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27430--27430
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27433--27433
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1723]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27516--27516
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27520--27520
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 27530--27530
[] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2),
phi[1]), pos=0, las=1)[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 27535--27535
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
[1724]
Underfull \hbox (badness 2922) in paragraph at lines 27571--27577
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27593--27593
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
[1725]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27609--27609
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 27623--27623
[]\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af
ter increasing maxiter !}[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27625--27625
[] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[]
Overfull \hbox (128.58029pt too wide) in paragraph at lines 27628--27628
[]\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, control = list(scaleOffset=1))[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 27630--27630
[] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1
e-11, nDcentral=TRUE), trace=TRUE)[]
[1726] [1727]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 27742--27742
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1728]
Underfull \hbox (badness 2922) in paragraph at lines 27804--27809
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27842--27842
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1729]
Underfull \hbox (badness 2922) in paragraph at lines 27891--27896
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1730]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27922--27922
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
Underfull \hbox (badness 2922) in paragraph at lines 27956--27961
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1731]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27981--27981
[]\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number
of iter...: 0" :[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27985--27985
[]\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28005--28005
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28015--28015
[] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x =
xmid = 2) = 2.5[]
[1732]
Underfull \hbox (badness 2922) in paragraph at lines 28050--28055
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28072--28072
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1733]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28090--28090
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
Underfull \hbox (badness 6493) in paragraph at lines 28142--28147
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1734]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28170--28170
[]\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 28173--28173
[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 28176--28176
[]\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 28179--28179
[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
[1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745]
[1746] [1747] [1748]
Underfull \hbox (badness 3396) in paragraph at lines 29062--29064
[]\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
[1749] [1750]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
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[]\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
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
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[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
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[]\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[]
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[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
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mon",[]
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pan.smth = 1/4)[]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
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[]\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was
given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
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v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\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:[]
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[]\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno
t compute exact p-value with ties[]
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[]\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9)
# same ties as (4:2, 3:1)[]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
= getOption("ts.eps"), ...)[]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
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[]\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 "")[]
[1804]) (./stats4-pkg.tex
Chapter 11.
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
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[]\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos
er to 0 and 1[]
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Chapter 12.
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[]
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[]\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i
ng any Tk or Tcl com-mand by sim-ply run-ning
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[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
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[][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep
t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/
n/10 (whose
[1836]) (./tools-pkg.tex
Chapter 13.
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
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[]\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n
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,
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin
e to use. Over-rides any
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
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xz"),[]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
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[] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[]
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[]\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[]
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\
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[]\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in-
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[]\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [
]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1
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[]\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu
r-rent pack-ages in the CRAN pack-age repos-i-
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iner in-for-ma-tion not pro-vided by
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[]\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR
AN_current_db []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[]
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[]\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests",
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor,
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio
n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the
pack-age
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[] \T1/pcr/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option
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[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
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\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-
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\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
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\T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
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[]\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str
ong",
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[]\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests",
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
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[]\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[]
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[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
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[]\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
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-
tor of links, as re-turned by
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
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[]\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10
, \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10
,
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
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[]\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5
.0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti
on
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[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts =
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[]\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/ptm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 4477--4483
[]\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 4477--4483
\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
[1905] [1906] [1907]
Underfull \hbox (badness 10000) in paragraph at lines 4703--4705
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10
, such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or
[1908]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733
[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[]
Underfull \hbox (badness 3240) in paragraph at lines 4746--4749
[]\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 ',
Underfull \hbox (badness 1742) in paragraph at lines 4750--4760
[]\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe
nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4788--4794
[]\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo
r R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4788--4794
\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 ',
[1909]
Underfull \hbox (badness 1571) in paragraph at lines 4816--4820
[]\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
Underfull \hbox (badness 2772) in paragraph at lines 4842--4847
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][
]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat
-ing ex-ist-ing
[1910] [1911]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4984--4984
[]\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[]
[1912]) (./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 `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
[1913] [1914] [1915] [1916]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 258--258
[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1917]
Underfull \hbox (badness 10000) in paragraph at lines 378--383
\T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min
imize",
[1918]
Underfull \hbox (badness 10000) in paragraph at lines 384--386
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow
han-dles, by de-fault pro-duced by
[1919]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450
[]\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F
irefox window[]
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[]\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
"Firefox"))[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469
[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1920] [1921] [1922]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683
[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
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[]\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 690--690
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691
[]\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 692--692
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Underfull \hbox (badness 10000) in paragraph at lines 726--732
[]\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 726--732
[]\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a
spell_package_C_files []\T1/ptm/m/n/10 per-form spell check-
[1923] [1924] [1925] [1926] [1927]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1049--1049
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1928]
Underfull \hbox (badness 1748) in paragraph at lines 1115--1123
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/pcr/m/n/
10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$
\T1/ptm/m/n/10 , in-di-cat-
Underfull \hbox (badness 2961) in paragraph at lines 1115--1123
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
Underfull \hbox (badness 1092) in paragraph at lines 1115--1123
\T1/ptm/m/n/10 as [][][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max", 1
) []\T1/ptm/m/n/10 which is []\T1/pcr/m/n/10 1 []\T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1115--1123
\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 1127--1129
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1929]
Underfull \hbox (badness 10000) in paragraph at lines 1235--1238
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1930] [1931]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1318--1318
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1932] [1933] [1934] [1935] [1936]
Underfull \hbox (badness 1859) in paragraph at lines 1721--1730
[]\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-
Underfull \hbox (badness 2042) in paragraph at lines 1721--1730
\T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1
/ptm/m/n/10 never re-turns. Do not re-port that
[1937] [1938]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1826--1826
[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[1939]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1861--1861
[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1940]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2007--2007
[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1941]
Underfull \hbox (badness 2277) in paragraph at lines 2076--2081
[]\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p
tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes
[1942]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2109--2109
[]\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct",
"upper", "xdigit")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2111--2111
[]\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2119--2119
[]\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
Unicode 13.)[]
[1943] [1944] [1945]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2267--2267
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1946]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2319--2319
[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1947] [1948]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2489--2489
[] \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")[]
[1949]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2512--2512
[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[1950]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2632--2632
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1951]
Underfull \hbox (badness 1082) in paragraph at lines 2706--2710
[][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab
out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file
s;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2711 ... the Clipboard in MS Windows}{clipboard}
[1952]
Underfull \hbox (badness 1163) in paragraph at lines 2742--2744
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1953]
Underfull \hbox (badness 10000) in paragraph at lines 2835--2837
[]\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
[1954] [1955] [1956] [1957]
Underfull \hbox (badness 10000) in paragraph at lines 3053--3055
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1958] [1959] [1960] [1961]
Underfull \hbox (badness 1762) in paragraph at lines 3346--3349
[]\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 []\T1/pcr/m/n/10 package =
[1962]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3438--3438
[]\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se
ts in the rpart package[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3439--3439
[]\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 '[]
[1963]
Underfull \hbox (badness 2452) in paragraph at lines 3515--3518
[]\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
[1964] [1965] [1966] [1967] [1968] [1969]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3931--3931
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[1970]
Underfull \hbox (badness 4779) in paragraph at lines 4010--4015
[]\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10
was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use
[1971]
Underfull \hbox (badness 1072) in paragraph at lines 4073--4077
[]\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
[1972]
Underfull \hbox (badness 7238) in paragraph at lines 4129--4134
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1
0 via \T1/ptm/m/n/10 the en-vi-ron-
Underfull \hbox (badness 1337) in paragraph at lines 4129--4134
\T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or
[]\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : /
/ curl . se / libcurl / c /
Underfull \hbox (badness 1184) in paragraph at lines 4144--4160
\T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10
'. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-
[1973]
Underfull \hbox (badness 4660) in paragraph at lines 4261--4264
\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
[1974]
Underfull \hbox (badness 10000) in paragraph at lines 4285--4287
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do
wnload.file[][][] []\T1/ptm/m/n/10 and
[1975] [1976]
Underfull \hbox (badness 1565) in paragraph at lines 4470--4474
[]\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
[1977]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4553--4553
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[1978]
Underfull \hbox (badness 1910) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p
le is run and
Underfull \hbox (badness 1655) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [
]\T1/ptm/m/n/10 sets the same state as
Underfull \hbox (badness 2846) in paragraph at lines 4587--4594
[]\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac
k-age's ex-am-ples. This is cur-
Underfull \hbox (badness 3460) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau
lt", "default",
Underfull \hbox (badness 1931) in paragraph at lines 4594--4601
[]\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di
-cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1979] [1980] [1981] [1982]
Underfull \hbox (badness 5939) in paragraph at lines 4840--4842
[]\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n
/10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault
[1983] [1984]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4983--4983
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1985]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.5054 ...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
<to be read again>
\relax
l.5054 ...mat Unordered and Ordered Lists}{format}
[1986] [1987] [1988]
[1989] [1990] [1991] [1992] [1993]
Underfull \hbox (badness 1622) in paragraph at lines 5577--5581
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
to ex-ter-nal GUIs or to the
[1994] [1995] [1996] [1997] [1998] [1999]
Underfull \hbox (badness 1448) in paragraph at lines 5956--5961
[]\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject
s, cor-re-spond-ing to call-ing
[2000] [2001]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 6106--6106
[]\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 6118--6118
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
[2002] [2003]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6251--6251
[] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 6252--6252
[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
[2004] [2005] [2006]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6462--6462
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[2007]
Underfull \hbox (badness 10000) in paragraph at lines 6546--6548
[]\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
[2008]
Underfull \hbox (badness 1502) in paragraph at lines 6595--6600
[]\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 6595--6600
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[2009] [2010]
Underfull \hbox (badness 10000) in paragraph at lines 6768--6777
[]\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 6768--6777
\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
[2011]
Underfull \hbox (badness 2150) in paragraph at lines 6832--6835
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
[2012]
Underfull \hbox (badness 5175) in paragraph at lines 6848--6851
[]\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc
h database for sub-se-quent use by
[2013]
Underfull \hbox (badness 3118) in paragraph at lines 6971--6973
[]\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
[2014] [2015] [2016]
Underfull \hbox (badness 5091) in paragraph at lines 7146--7148
[]\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 10000) in paragraph at lines 7176--7183
[]\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends
", "Imports", "LinkingTo",
Underfull \hbox (badness 10000) in paragraph at lines 7176--7183
\T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports",
Underfull \hbox (badness 1270) in paragraph at lines 7176--7183
\T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in
-stalls all the pack-ages
Underfull \hbox (badness 1270) in paragraph at lines 7191--7201
\T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla
g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If
[2017]
Underfull \hbox (badness 4441) in paragraph at lines 7234--7237
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed to
Underfull \hbox (badness 2837) in paragraph at lines 7234--7237
[]\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall.
E.g., []\T1/pcr/m/n/10 c("--html",
Underfull \hbox (badness 1424) in paragraph at lines 7242--7245
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
[2018]
Underfull \hbox (badness 2376) in paragraph at lines 7313--7320
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n
/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7313--7320
\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 7313--7320
\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 1087) in paragraph at lines 7321--7324
[]\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt
m/m/n/10 al-ways works pro-vided the pack-age con-tains no
[2019]
Underfull \hbox (badness 1314) in paragraph at lines 7401--7408
[]\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute
all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 7481--7486
[][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac
kages[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7504--7504
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
[2021]
Underfull \hbox (badness 5133) in paragraph at lines 7540--7544
[]\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 7554--7557
[]\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10
DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7601--7601
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[2022] [2023]
Underfull \hbox (badness 4132) in paragraph at lines 7725--7727
[]\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
[2024] [2025] [2026]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7892--7892
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[2027] [2028] [2029]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8035--8035
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
Underfull \hbox (badness 10000) in paragraph at lines 8075--8077
[]\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
[2030] [2031]
Underfull \hbox (badness 10000) in paragraph at lines 8180--8182
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
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[]\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 S3 class
[2032] [2033] [2034] [2035]
Underfull \hbox (badness 1859) in paragraph at lines 8413--8416
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
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\T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/
n/10 el-e-ments with names start-ing with a suit-able pre-fix
[2036]
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[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d
b"[]\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 8518--8518
[]\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8526--8526
[]\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 8534--8534
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[2037] [2038]
Underfull \hbox (badness 1917) in paragraph at lines 8621--8623
[]\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/
n/10 ,
[2039] [2040] [2041] [2042]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8893--8893
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8894--8894
[] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8895--8895
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[2043]
Underfull \hbox (badness 10000) in paragraph at lines 8923--8925
[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\
T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 8937--8939
[]\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut
, al-low-ing things like []\T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8945--8950
[]\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,
[2044]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8991--8991
[] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8992--8992
[] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[]
[2045] [2046]
Underfull \hbox (badness 10000) in paragraph at lines 9121--9126
[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade",
Underfull \hbox (badness 10000) in paragraph at lines 9128--9131
[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("installed", "not
[2047]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
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[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[2048] [2049] [2050]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9418--9418
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[2051]
Underfull \hbox (badness 1789) in paragraph at lines 9551--9553
[]\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
[2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060]
Underfull \hbox (badness 5203) in paragraph at lines 10124--10127
[]\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
[2061] [2062] [2063]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10374--10374
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[2064] [2065]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10535--10535
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[2066] [2067] [2068]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10716--10716
[]\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[]
[2069]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10802--10802
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10805--10805
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10810--10810
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2070]
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[]\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force
s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL
[2071] [2072] [2073] [2074]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11161--11161
[]\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC",
"HPD"),
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[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
Underfull \hbox (badness 10000) in paragraph at lines 11169--11174
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 11169--11174
\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 11169--11174
[]\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER
S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2075] [2076] [2077] [2078]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11402--11402
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2079] [2080] [2081] [2082]
Underfull \hbox (badness 10000) in paragraph at lines 11663--11667
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11681--11681
[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[]
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[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[2083] [2084]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11819--11819
[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 11820--11820
[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
[2085] [2086]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11955--11955
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[2087] [2088]
Underfull \hbox (badness 1917) in paragraph at lines 12087--12090
[]\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n
ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me
nt vari-
Underfull \hbox (badness 4328) in paragraph at lines 12087--12090
\T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10
. If this is set, then it takes prece-dence over
Overfull \hbox (106.98032pt too wide) in paragraph at lines 12110--12110
[]\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 '[]
[2089]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 12202--12202
[] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news",
"Rfunctions",[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12203--12203
[] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig
nettes"),[]
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[] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s
ubject",[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 12206--12206
[] \T1/pcr/m/n/10 "subject:descending", "size", "size:de
scending"),[]
[2090]
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\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 2662) in paragraph at lines 12229--12237
\T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re
-verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12274--12274
[]\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes","
Rfunctions"))[]
[2091]
Underfull \hbox (badness 1377) in paragraph at lines 12330--12333
[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/
m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style
[2092]
Underfull \hbox (badness 3646) in paragraph at lines 12365--12367
[][][]$\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 /
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12403--12403
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[2093] [2094] [2095]
Underfull \hbox (badness 10000) in paragraph at lines 12585--12589
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i
s now taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12618--12624
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][]
[]\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m
/n/10 out-put in
[2096] [2097]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12794--12794
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[2098]
Underfull \hbox (badness 1009) in paragraph at lines 12812--12824
[]\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
Underfull \hbox (badness 2600) in paragraph at lines 12852--12854
[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows
and
[2099]
Underfull \hbox (badness 1043) in paragraph at lines 12895--12900
[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
con-fig-ured the map-ping of font num-bers to fonts, and
[2100] [2101] [2102] [2103]
Underfull \hbox (badness 1888) in paragraph at lines 13188--13191
[]\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-der. Where
Underfull \hbox (badness 10000) in paragraph at lines 13205--13208
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2104]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13251--13251
[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
[2105]
Underfull \hbox (badness 2158) in paragraph at lines 13306--13309
[]\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
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13354--13354
[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
[2106] [2107] [2108]
Underfull \hbox (badness 2302) in paragraph at lines 13511--13513
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2109]
Underfull \hbox (badness 3333) in paragraph at lines 13619--13621
[]\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir
ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2110] [2111] [2112]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 13786--13786
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
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[]\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
[][][]\T1/pcr/m/n/10 deparse[][][](control = <S>) []\T1/ptm/m/n/10 will not ha
ve
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha
s only a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic
h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it
y rea-sons;
[2113]
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[]\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau
lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to
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[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2114]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
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[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
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[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[2115] [2116] [2117]
Underfull \hbox (badness 10000) in paragraph at lines 14094--14096
[]\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
[2118]
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[]\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se
e
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[][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/
m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu-
[2119]
Underfull \hbox (badness 6300) in paragraph at lines 14252--14259
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau
lt) then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 14252--14259
\T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt
m/m/n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 14252--14259
\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
[2120] [2121]
Underfull \hbox (badness 2020) in paragraph at lines 14417--14425
\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 plat-forms),
Underfull \hbox (badness 1194) in paragraph at lines 14417--14425
\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --
exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n
/10 ' (and sim-i-lar) and on Win-dows
[2122]
Underfull \hbox (badness 1622) in paragraph at lines 14426--14433
[]\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p
cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able
[2123]
Underfull \hbox (badness 5022) in paragraph at lines 14567--14571
[]\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t
o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment
vari-able
Underfull \hbox (badness 10000) in paragraph at lines 14574--14577
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 14574--14577
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
[2124] [2125] [2126]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14740--14740
[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
[2127] [2128] [2129] [2130] [2131] [2132]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15181--15181
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15187--15187
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Underfull \hbox (badness 4467) in paragraph at lines 15208--15210
[]\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 15223--15227
\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
[2133]
Underfull \hbox (badness 1694) in paragraph at lines 15237--15241
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins
talled.packages[][][](lib.loc =
Underfull \hbox (badness 10000) in paragraph at lines 15243--15248
[]\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 15243--15248
\T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15243--15248
[]\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac
he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][]
Underfull \hbox (badness 1052) in paragraph at lines 15249--15251
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
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[]\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n
/10 available.packages(contriburl =
Underfull \hbox (badness 1226) in paragraph at lines 15279--15284
\T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa
ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
Underfull \hbox (badness 10000) in paragraph at lines 15300--15305
[]\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
[2134]
Underfull \hbox (badness 10000) in paragraph at lines 15308--15311
[][][]\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.pa
ckages[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15362--15362
[]\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt")
[2135] [2136] [2137]
Underfull \hbox (badness 2293) in paragraph at lines 15569--15572
[][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v
i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,
[2138]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 15585--15585
[]\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:[]
[2139]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15652--15652
[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
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[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
[2140] [2141]
Underfull \hbox (badness 1297) in paragraph at lines 15805--15807
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2142]
Underfull \hbox (badness 4036) in paragraph at lines 15852--15854
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil
l delete a menu and all of its items and sub-menus.
[2143] [2144]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15972--15972
[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2145]
Underfull \hbox (badness 1715) in paragraph at lines 16024--16027
[]\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : []
\T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n
/10 and
Underfull \hbox (badness 10000) in paragraph at lines 16069--16071
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. []\T1/pcr/m/n/10 file =
[2146] [2147] [2148]) [2149] [2150] (./KernSmooth-pkg.tex
Chapter 15.
[2151]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 123--123
[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2152] [2153] [2154] [2155] [2156]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2157] [2158] [2159] [2160]) (./MASS-pkg.tex
Chapter 16.
[2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182]
[2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193]
[2194]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2418--2418
[]\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 2422--2422
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[2195] [2196] [2197] [2198]
Underfull \hbox (badness 6559) in paragraph at lines 2701--2704
[]\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
[2199] [2200] [2201]
Underfull \hbox (badness 10000) in paragraph at lines 2871--2876
[]\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo
gnormal"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2871--2876
[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi
al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
/10 "Poisson"[]\T1/ptm/m/n/10 ,
[2202] [2203]
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[]\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
[2204] [2205] [2206]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3234--3234
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
[2207]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv
et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and
[2220] [2221] [2222] [2223] [2224] [2225] [2226]
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",
...)[]
[2227] [2228] [2229]
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,
[2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]
[2241] [2242] [2243]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5930--5930
[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2244]
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[]\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")
[2245] [2246]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6151 ...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
<to be read again>
\relax
l.6151 ...sical N, P, K Factorial Experiment}{npk}
[2247] [2248] [2249]
[2250] [2251] [2252]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6571--6571
[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2253]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2254] [2255] [2256] [2257] [2258] [2259]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7098--7098
[]\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 7115--7115
[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
[2260]
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[]\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 ) =
[2261]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2262] [2263]
Underfull \hbox (badness 1389) in paragraph at lines 7372--7375
[]\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than
[]\T1/pcr/m/n/10 min(p,
[2264] [2265]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7502--7502
[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2266]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7567--7567
[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2267] [2268] [2269] [2270] [2271] [2272]
Underfull \hbox (badness 4686) in paragraph at lines 8005--8007
[]\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
[2273] [2274]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8124--8124
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
Underfull \hbox (badness 1590) in paragraph at lines 8148--8152
[]\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
[2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285]
[2286] [2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9529--9529
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2295]
Underfull \hbox (badness 2035) in paragraph at lines 9641--9643
[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\
T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n
/10 ,
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[]\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-l
arly),
[2296]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9738--9738
[]\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 9740--9740
[]\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 9743--9743
[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2297] [2298] [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] [2307]
[2308] [2309]) (./Matrix-pkg.tex [2310]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 35--38
[]\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 35--38
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2311]
Underfull \hbox (badness 1769) in paragraph at lines 89--92
[]\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
[2312]
Underfull \hbox (badness 2229) in paragraph at lines 153--156
[]\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 153--156
\T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor
, these ar-gu-ments will be con-cate-nated to a new
[2313]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 262--264
[]\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
[2314] [2315]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 445--445
[] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym
metry property[]
[2316]
Underfull \hbox (badness 5119) in paragraph at lines 488--492
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Overfull \hbox (4.38043pt too wide) in paragraph at lines 522--522
[]\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 524--524
[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
[2317]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 533--533
[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2318]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 647--647
[]\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 648--648
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>) 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 649--649
[]\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}"}.[]
[2319]
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[] \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?[]
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[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
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[]\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[]
[2320]
Underfull \hbox (badness 1874) in paragraph at lines 737--740
[]\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 https : / / netlib . org /
[2321] [2322]
Underfull \hbox (badness 1107) in paragraph at lines 860--865
\T1/ptm/m/n/10 sity'' of []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/
10 y[]\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n/10 code in []
\T1/pcr/m/n/10 selectMethod(cbind2,
Underfull \hbox (badness 10000) in paragraph at lines 903--908
[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/
10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met
h-ods:
[2323]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 967--967
[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2324]
Underfull \hbox (badness 3612) in paragraph at lines 1054--1057
[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "pMatrix") []\T1/ptm/m/n/10
re-turns the per-mu-ta-tion
[2325]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1154 ...- '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
<to be read again>
\relax
l.1154 ...- 'Matrix' S4 Generic and Methods}{chol}
[2326] [2327]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1301--1301
[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2328]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1396--1396
[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
[2329]
Underfull \hbox (badness 2277) in paragraph at lines 1424--1427
[]\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
[2330]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\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(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529
[]\T1/pcr/m/n/9 str(re <- lapply(rr, expand), max.level=2) ## each has a \TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 matrix[]
[2331]
Underfull \hbox (badness 10000) in paragraph at lines 1565--1572
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("Cholesky", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 4673) in paragraph at lines 1565--1572
[]\T1/pcr/m/n/10 new("BunchKaufman", ...)[]\T1/ptm/m/n/10 , etc, or rather by c
alls of the form [][][]\T1/pcr/m/n/10 chol[][][](pm) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1600--1604
[]\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
[2332]
Underfull \hbox (badness 1221) in paragraph at lines 1616--1622
\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 .
Hence, for com-pat-i-bil-ity, the []\T1/pcr/m/n/10 "Cholesky" []\T1/ptm/m/n/10
and
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
has been already used, duplicate ignored
<to be read again>
\relax
l.1657 ... 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
<to be read again>
\relax
l.1657 ... 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
<to be read again>
\relax
l.1658 \aliasA{colMeans}{colSums}{colMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1681 \aliasA{rowMeans}{colSums}{rowMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1694 \aliasA{rowSums}{colSums}{rowSums}
[2333pdfTeX warning (ext4): destinati
on with the same identifier (name{Rfn.rowMeans,diagonalMatrix.Rdash.method}) ha
s been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.1733 ## S4 method for signature 'CsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.rowSums,diagonalMatrix.Rdash.method}) h
as been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.1733 ## S4 method for signature 'CsparseMatrix'
]
Underfull \hbox (badness 2922) in paragraph at lines 1750--1754
[]\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 1750--1754
\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 fr
om a
Underfull \hbox (badness 1237) in paragraph at lines 1761--1764
[][][]\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/1
0 , since
[2334] [2335]
Underfull \hbox (badness 3547) in paragraph at lines 1915--1918
[]\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
[2336] [2337] [2338] [2339] [2340] [2341]
Underfull \hbox (badness 7379) in paragraph at lines 2445--2447
[]\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
[2342] [2343] [2344]
Underfull \hbox (badness 10000) in paragraph at lines 2696--2699
[]\T1/pcr/m/n/10 signature(from = "dgTMatrix", to = "matrix")[]\T1/ptm/m/n/10 ,
and typ-i-cally co-er-cion
Underfull \hbox (badness 4846) in paragraph at lines 2721--2725
[]\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and []
[][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr
/m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 2726--2730
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2733--2736
[]\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 a
nd [][][]\T1/pcr/m/n/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 ;
[2345]
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[] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE,
kind)[]
Underfull \hbox (badness 2689) in paragraph at lines 2789--2791
[]\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 2793--2798
[]\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 2793--2798
[][][]\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
[2346]
Underfull \hbox (badness 1097) in paragraph at lines 2816--2819
[]\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 ldiMat
rix[][][] []\T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2829--2834
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][] []\T1/ptm/m/n/10 (the re-sult-ing clas
s de-pend-ing on []\T1/pcr/m/n/10 shape []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 k
ind[]\T1/ptm/m/n/10 ) rep-re-sen-ta-tion of
[2347]
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[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a []
[][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma
trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 6542) in paragraph at lines 2960--2964
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr
oup meth-ods re-turn a
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10
: the re-sult is from class
[2348pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coer
ce,diagonalMatrix,nMatrix.Rdash.method}) has been already used, duplicate ignor
ed
<argument> ...shipout:D \box_use:N \l_shipout_box
l.2975
]
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[]\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j
ect of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 2986--2990
[][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes
e 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
[2349] [2350]
Underfull \hbox (badness 10000) in paragraph at lines 3166--3168
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 :
this group con-tains
[2351] [2352]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe
rent from the random one[]
[2353]
Underfull \hbox (badness 2469) in paragraph at lines 3422--3425
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][]
[]\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/
ptm/m/n/10 , via
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[]\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as
Underfull \hbox (badness 2020) in paragraph at lines 3445--3450
[][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10
for ef-fi-ciency rea-sons only check the di-
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\T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p
tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion
Underfull \hbox (badness 1590) in paragraph at lines 3451--3460
\T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][
][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see
[]\T1/pcr/m/n/10 selectMethod("coerce",
[2354] [2355]
Underfull \hbox (badness 10000) in paragraph at lines 3599--3603
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsCMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 2103) in paragraph at lines 3599--3603
[]\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v
ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 ,
[2356]
Underfull \hbox (badness 1571) in paragraph at lines 3649--3652
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10
: Re-turns (and stores) the
[2357] [2358]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3818
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class []
\T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse
Matrix"[]\T1/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3813--3818
\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 "compMatri
x" []\T1/ptm/m/n/10 by class
Underfull \hbox (badness 1400) in paragraph at lines 3825--3828
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10
: if []\T1/pcr/m/n/10 uplo ==
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 3896--3898
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsyMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1365) in paragraph at lines 3938--3941
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10
, or []\T1/pcr/m/n/10 x = "dsyMatrix"
[2360]
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[]\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ
internally :[]
[2361]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4116--4116
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
[2362]
Underfull \hbox (badness 3635) in paragraph at lines 4179--4183
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla
ss
Underfull \hbox (badness 10000) in paragraph at lines 4188--4191
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
[2363]
Underfull \hbox (badness 10000) in paragraph at lines 4193--4197
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n
/10 : the
[2364] [2365pdfTeX warning (ext4): destination with the same identifier (name{R
fn.coerce,dtrMatrix,dgeMatrix.Rdash.method}) has been already used, duplicate i
gnored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.4347 \item[\code{diag}:]
Object of class \code{"character"}. Must be]
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[]\T1/pcr/m/n/10 signature(a = "dtrMatrix", b = "....")[]\T1/ptm/m/n/10 efficie
ntely use a ``for-ward-solve'' or
[2366] [2367] [2368] [2369]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 4635--4635
[]\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe
ll-Boeing/counterx/counterx.html[]
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[] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB
/Boeing/msc00726.tar.gz"))))[]
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[]\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary
dir./folder:[]
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[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
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[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2370] [2371] [2372] [2373]
Underfull \hbox (badness 10000) in paragraph at lines 4937--4942
[]\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10
, and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][
][][]\T1/ptm/m/n/10 ,
[2374]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5018--5018
[]\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons"
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[] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2,
dimnames=dns))[]
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[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2375]
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[] \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 '[]
[2376] [2377]
Underfull \hbox (badness 4120) in paragraph at lines 5170--5173
[]\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
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5188--5188
[]\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) #
failed for 2 days ..[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5208--5208
[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
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[] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,
border.col=NA)[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5215--5215
[] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[]
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5219--5219
[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
[2378]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227
[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2379]
Underfull \hbox (badness 1817) in paragraph at lines 5326--5335
[]\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 wit
hin the
Underfull \hbox (badness 10000) in paragraph at lines 5368--5370
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
Underfull \hbox (badness 7081) in paragraph at lines 5370--5373
[]\T1/pcr/m/n/10 signature(from = "integer", to = "indMatrix")[]\T1/ptm/m/n/10
: This en-ables typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : T
he list must have two
[2380]
Underfull \hbox (badness 3302) in paragraph at lines 5401--5404
[]\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 :
re-turn the kro-necker
[2381] [2382] [2383] [2384]
Overfull \hbox (138.78088pt too wide) in paragraph at lines 5776--5776
[]\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, tol1 = 8
* tol, checkDN = TRUE, ...)[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5782--5782
[]\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, checkDN
= TRUE, ...)[]
[2385]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5841--5841
[]\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if
not "formally"[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5845--5845
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g
eneric from base[]
[2386]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5937--5937
[]\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even
if not "formally"[]
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[]\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames
= FALSE)
[2387] [2388]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042
[]\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 6043--6043
[] \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 6050--6050
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2389] [2390]
Underfull \hbox (badness 1062) in paragraph at lines 6204--6207
[]\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 6233--6236
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2391]
Underfull \hbox (badness 2635) in paragraph at lines 6402--6407
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ldenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6402--6407
\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 "Matri
x"[]\T1/ptm/m/n/10 , by class
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 6410--6413
[]\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.,
Underfull \hbox (badness 10000) in paragraph at lines 6566--6576
[]\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T
1/ptm/m/n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6566--6576
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc
r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10
, and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\
T1/ptm/m/n/10 --in
[2393]
Underfull \hbox (badness 3179) in paragraph at lines 6648--6651
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2394]
Underfull \hbox (badness 10000) in paragraph at lines 6751--6754
[]\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.,
[2395]
Underfull \hbox (badness 10000) in paragraph at lines 6830--6833
[]\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.,
[2396]
Underfull \hbox (badness 1430) in paragraph at lines 6904--6910
\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, []\T1/pcr/
m/n/10 lu(x,
[2397]
Underfull \hbox (badness 1675) in paragraph at lines 6929--6932
[]\T1/pcr/m/n/10 lu() []\T1/ptm/m/n/10 is a generic func-tion with spe-cial met
h-ods for dif-fer-ent types of ma-tri-ces. Use
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[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2398] [2399]
Underfull \hbox (badness 10000) in paragraph at lines 7141--7144
[]\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm
/m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x
,
[2400]
Underfull \hbox (badness 1490) in paragraph at lines 7163--7165
[]\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/
m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][
] []\T1/ptm/m/n/10 and (one case of)
[2401] [2402]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again>
\relax
l.7358 \aliasA{det}{Matrix-class}{det}
[2403pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.coerce,Matrix,denseMatrix.Rdash.method}) has
been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.7439 \item[dim]
\code{signature(x = "Matrix")}: extract matrix dimensions]
Underfull \hbox (badness 1337) in paragraph at lines 7446--7449
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set
the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a
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Underfull \hbox (badness 10000) in paragraph at lines 7469--7471
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This
re-lies on a cor-rect
[2404]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.7532 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again>
\relax
l.7629 ...A{crossprod}{matrix-products}{crossprod}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again>
\relax
l.7723 ...tcrossprod}{matrix-products}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 7816--7822
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/
pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2405]
Underfull \hbox (badness 10000) in paragraph at lines 7889--7892
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 10000) in paragraph at lines 7892--7897
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
Underfull \hbox (badness 3557) in paragraph at lines 7892--7897
[]\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr
ix mul-ti-pli-ca-tion. Mul-ti-
Underfull \hbox (badness 6608) in paragraph at lines 7897--7901
\T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas
s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 1552) in paragraph at lines 7907--7908
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-
[2406] [2407] [2408]
Underfull \hbox (badness 1062) in paragraph at lines 8087--8090
[]\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2409]
Underfull \hbox (badness 3312) in paragraph at lines 8177--8179
[]\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 []\T1/pcr/m/n/10 X <-
[2410] [2411]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 8279--8279
[] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[]
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[]\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 [2412]
Underfull \hbox (badness 2635) in paragraph at lines 8386--8391
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ndenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 8386--8391
\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 "Matri
x"[]\T1/ptm/m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 8394--8397
[]\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.,
[2413]
Underfull \hbox (badness 2521) in paragraph at lines 8464--8470
[]\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N
ote that these co-er-cions
[2414]
Underfull \hbox (badness 1867) in paragraph at lines 8586--8588
[]\T1/ptm/m/n/10 fast sim-
[2415]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8626 \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
<to be read again>
\relax
l.8626 \HeaderA{norm}{Matrix Norms}{norm}
[2416]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8719--8719
[]\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 8720--8720
[]\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 8721--8721
[]\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 8867--8877
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n
/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri
x[]\T1/ptm/m/n/10 ,
[2417]
Underfull \hbox (badness 3179) in paragraph at lines 8938--8941
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2418]
Underfull \hbox (badness 10000) in paragraph at lines 9036--9039
[]\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.,
[2419]
Underfull \hbox (badness 10000) in paragraph at lines 9118--9121
[]\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.,
[2420] [2421]
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[]\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "missing", dr
op =
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[]\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "missing", drop
=
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[]\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "missing", drop
=
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[]\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "missing", dro
p =
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[]\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "missing", dr
op =
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[]\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "NULL", drop
=
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op =
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p =
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[2423]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") []\T1/ptm/m/n/10 and ot
her sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "integer", to = "pMatrix")[]\T1/ptm/m/n/10 :
This is en-ables typ-i-cal
[2424]
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "matrix")[]\T1/ptm/m/n/10 : c
o-er-cion to a tra-di-tional
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[]\T1/pcr/m/n/10 signature(x = "pMatrix", logarithm="logical")[]\T1/ptm/m/n/10
: Since per-mu-ta-
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\T1/ptm/m/n/10 trix; note that []\T1/pcr/m/n/10 solve(P) []\T1/ptm/m/n/10 is id
en-ti-cal to []\T1/pcr/m/n/10 t(P) []\T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-c
es. See
[2425]
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[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of []
\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2426] [2427]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.9569 \aliasA{qr}{qr-methods}{qr}
[2428]
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[]\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![]
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[]\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[]
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[]\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[]
[2429]
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[]\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10
qr[][][](x, tol,
[2430]
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 , it cor-re-sponds to
[2431]
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[]\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"[]
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[]\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol
= 1e-7)) # all 14[]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war
ning+ ~1.5 sec (2013)[]
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[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
[2432]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco
nd}) has been already used, duplicate ignored
<to be read again>
\relax
l.9893 ... the Reciprocal Condition Number}{rcond}
[2433]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2434] [2435] [2436]
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\T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr
ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n
/10 is not
[2437] [2438]
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class []\T1/pcr/m/n
/10 "Matrix"[]\T1/ptm/m/n/10 ) or tra-di-tional
[2439]
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[] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[]
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[]\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[]
[2440]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.10470 \aliasA{solve}{solve-methods}{solve}
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[]\T1/pcr/m/n/10 ## solve(a, b, ...) # the two-argument version, almost always
preferred to
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[]\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "
D", "P", "Pt"), ...)[]
[2441]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 solve []\T1/ptm/m/n/10 meth-ods for a
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[]\T1/ptm/m/n/10 (for all []\T1/pcr/m/n/10 b[]\T1/ptm/m/n/10 ) work via []\T1/p
cr/m/n/10 as(a,
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 (
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 (
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\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-met-ric,
[2442]
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
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[]\T1/ptm/m/n/10 works via []\T1/pcr/m/n/10 as(b,
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via []\T1/pcr/m/n/10 as(a,
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[][][]\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
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 sparseLU[][][][]\T1/ptm/m/n/10 ,
and
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[]\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2443]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs
parse)[]
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs
parse,[]
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[]\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,
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[]\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)
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[]\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c
on-trasts to be ap-plied to the
[2444]
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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[]\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
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2445]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2446] [2447]
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[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
[2448]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2449]
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[]\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
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[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
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[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2450]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\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)[]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[]
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[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
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[]\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\
T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods
[2452]
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[][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences,
such 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
<to be read again>
\relax
l.11486 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2453] [2454]
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[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")[]\T1/ptm/m/n/10 : For []\
T1/pcr/m/n/10 solve(a,b)[]\T1/ptm/m/n/10 , sim-ply uses
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[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
[2455]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
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[]\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-
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\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 "
lsparseVector"[]\T1/ptm/m/n/10 ,
[2456]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/
n/10 co-erces sparse
[2457]
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[]\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
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str
uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*,
[2458] [2459]
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[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more
usual con-struc-tor of such ma-tri-ces. Then,
[2460]
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[]\T1/pcr/m/n/10 signature(from = "ddiMatrix", to = "symmetricMatrix")[]\T1/ptm
/m/n/10 : and many
[2461]
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\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-m
eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
Underfull \hbox (badness 2057) in paragraph at lines 12207--12209
[]\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.,
[2462] [2463]
Underfull \hbox (badness 6641) in paragraph at lines 12294--12297
[]\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 ) h
ave meth-ods with
Underfull \hbox (badness 5133) in paragraph at lines 12338--12342
[]\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 12338--12342
\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
[2464] [2465]
Underfull \hbox (badness 7649) in paragraph at lines 12445--12447
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2466] [2467]
Underfull \hbox (badness 10000) in paragraph at lines 12563--12565
[]\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 ,
though
[2468]
Underfull \hbox (badness 1668) in paragraph at lines 12692--12695
[][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac
k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac
kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes
[2469]
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[]\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
[2470]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12781--12781
[]\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 12782--12782
[]\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)[]
[2471] [2472]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12936--12936
[] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/
x))$modulus))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12941--12941
[] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/
x))$modulus))[]
[2473]
Underfull \hbox (badness 6910) in paragraph at lines 13147--13149
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2474]
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref) removing `\Rpercent' on input line 13194.
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref) removing `\Rpercent' on input line 13194.
[2475]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13312--13312
[]\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero
s" to drop0()[]
[2476]) (./boot-pkg.tex
Chapter 18.
[2477] [2478] [2479] [2480] [2481] [2482] [2483]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532
[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2484]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\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 585--590
[]\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-
[2485] [2486] [2487]
Underfull \hbox (badness 1881) in paragraph at lines 826--828
[]\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 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo
ot.ci[][][][]\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 j
ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T
1/ptm/m/n/10 ,
[2488]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887
[]\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 [2489]
[2490] [2491]
Underfull \hbox (badness 1496) in paragraph at lines 1084--1093
[]\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 1084--1093
\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 1084--1093
\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 1105--1111
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2492] [2493] [2494] [2495]
Underfull \hbox (badness 1571) in paragraph at lines 1445--1447
[]\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-
[2496] [2497] [2498] [2499] [2500]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2501] [2502] [2503]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2505]
Underfull \hbox (badness 6268) in paragraph at lines 2084--2086
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2506] [2507] [2508]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\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
[2509]
Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat
istic []\T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2432--2434
[]\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 2440--2441
[][][]\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 ,
[2510] [2511]
Underfull \hbox (badness 1077) in paragraph at lines 2536--2540
[]\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/1
0 is the sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2536--2540
\T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr
/m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T
1/ptm/m/n/10 is used. This is mul-ti-plied by
[2512] [2513] [2514] [2515] [2516]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
[]\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 2897--2897
[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2517] [2518] [2519]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr
ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/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 ,
[2520]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2521] [2522] [2523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2524] [2525] [2526] [2527] [2528] [2529] [2530]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2531] [2532]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2533] [2534] [2535] [2536]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2537] [2538]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\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 4371--4375
\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the
r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a
re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to
[2539] [2540] [2541] [2542] [2543] [2544] [2545] [2546] [2547]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2548] [2549] [2550] [2551]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\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 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2552]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2561]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
[]\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less
than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then
[2562]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s
addle.distn"[]\T1/ptm/m/n/10 . See the help file for
[2563] [2564] [2565] [2566]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
[]\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 6497--6497
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2569] [2570] [2571]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\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
[2572] [2573]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2574] [2575] [2576] [2577] [2578] [2579] [2580] [2581]) (./class-pkg.tex
[2582]
Chapter 19.
[2583] [2584] [2585] [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593]
[2594] [2595] [2596] [2597] [2598]) (./cluster-pkg.tex
Chapter 20.
[2599] [2600] [2601]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253
[] \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 254--254
[] \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 255--255
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2602] [2603]
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[2605]
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[] \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 523--523
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2606] [2607]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638
[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
[2608]
Underfull \hbox (badness 3078) in paragraph at lines 691--694
[]\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
[2609] [2610]
Underfull \hbox (badness 2941) in paragraph at lines 791--794
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\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 ,
[2611]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
Underfull \hbox (badness 10000) in paragraph at lines 881--883
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2612]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2613]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2614] [2615]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1121--1121
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1138--1138
[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 1176--1176
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
Underfull \hbox (badness 4144) in paragraph at lines 1208--1212
[]\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
[2617]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1284--1284
[] \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 1290--1290
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2618] [2619] [2620]
Underfull \hbox (badness 10000) in paragraph at lines 1477--1480
Underfull \hbox (badness 10000) in paragraph at lines 1494--1498
[][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds
cale[][][][]\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/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1518--1518
[]\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 1528--1528
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2621]
Underfull \hbox (badness 5741) in paragraph at lines 1568--1571
[]\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d
er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2622]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1637--1637
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2623]
Underfull \hbox (badness 1552) in paragraph at lines 1686--1688
[]\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n
/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se
e
Underfull \hbox (badness 1629) in paragraph at lines 1699--1703
[]\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault
\T1/ptm/m/n/10 for all nu-meric
Underfull \hbox (badness 3746) in paragraph at lines 1699--1703
\T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T
1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r
e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see
[2624]
Underfull \hbox (badness 1540) in paragraph at lines 1775--1783
\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 $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 =
[2625]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1867--1867
[]\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1886--1886
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2626] [2627] [2628] [2629] [2630]
Underfull \hbox (badness 10000) in paragraph at lines 2207--2210
Underfull \hbox (badness 3179) in paragraph at lines 2221--2227
[][][]\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/1
0 ellipsoid []\T1/ptm/m/n/10 ob-jects.
[2631] [2632]
Underfull \hbox (badness 10000) in paragraph at lines 2379--2382
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2633]
Underfull \hbox (badness 1292) in paragraph at lines 2447--2450
[]\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10
, the num-ber of it-er-a-tions needed and
[2634]
Underfull \hbox (badness 6675) in paragraph at lines 2456--2458
[]\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 2479--2482
[][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f
anny[][][][]\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 ,
[2635] [2636]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 2608--2608
[]\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES
= FALSE, ...)
[2637]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 2655--2655
[] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k
<= k, table(cl.k) >= 2)[]
[2638]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2760--2760
[]\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 ):[]
[2639]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2839--2839
[] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[]
[2640] [2641] [2642]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2643] [2644]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3171--3171
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2645] [2646] [2647]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3367--3367
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3368--3368
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2648]
Underfull \hbox (badness 10000) in paragraph at lines 3435--3438
[]\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 []\T1/pcr/m/n/10 dg <-
[2649]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3485--3485
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3486--3486
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2650] [2651] [2652]
Underfull \hbox (badness 10000) in paragraph at lines 3671--3674
[]\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 [][][]\T1/pcr/m/n/10 pam[]
[][](*,
Underfull \hbox (badness 1448) in paragraph at lines 3671--3674
\T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p
tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is
[2653]
Underfull \hbox (badness 10000) in paragraph at lines 3734--3739
[][][]\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.de
fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 ,
[2654]
Underfull \hbox (badness 1748) in paragraph at lines 3796--3801
\T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p
tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx
<-
Underfull \hbox (badness 6268) in paragraph at lines 3808--3811
[][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o
bject[][][][]\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/1
0 hclust[][][][]\T1/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 ,
[2655] [2656] [2657]
Underfull \hbox (badness 10000) in paragraph at lines 3993--3996
[][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag
nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4024--4027
[][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl
ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2658]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4077--4077
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
[2659]
Underfull \hbox (badness 2035) in paragraph at lines 4088--4090
[]\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
[2660] [2661] [2662]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4281--4281
[] \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 4283--4283
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2663] [2664]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4426--4426
[]\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 4435--4435
[] \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 4437--4437
[] \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 4440--4440
[]\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 4442--4442
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4449--4449
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2665] [2666] [2667] [2668] [2669] [2670] [2671]
Underfull \hbox (badness 10000) in paragraph at lines 4823--4829
[]\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i
s slightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4839--4841
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4852--4852
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4854--4854
[]\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s medoid indices == pam(xclara, 3)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4864--4864
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2672]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4868--4868
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2673]) (./codetools-pkg.tex [2674]
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,[]
[2675]
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 checkUsage
Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2676]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2677] [2678] [2679]) (./foreign-pkg.tex [2680]
Chapter 22.
Underfull \hbox (badness 10000) in paragraph at lines 33--37
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2681]
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
[2682] [2683]
Underfull \hbox (badness 3601) in paragraph at lines 237--245
[]\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 ,
[2684]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295
[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2685] [2686] [2687]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2688]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462
[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 2846) in paragraph at lines 505--514
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-ent lev-
Underfull \hbox (badness 3746) in paragraph at lines 505--514
\T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul
t), the first orig-i-nal value la-bel is
Underfull \hbox (badness 2269) in paragraph at lines 505--514
\T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p
cr/m/n/10 paste0(label,
Underfull \hbox (badness 10000) in paragraph at lines 515--518
[]\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 515--518
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup
licated_"[]\T1/ptm/m/n/10 ) if
[2689]
Underfull \hbox (badness 10000) in paragraph at lines 550--558
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com /
en-[]us / windows / win32 / intl /
Underfull \hbox (badness 7613) in paragraph at lines 568--574
[]\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
[2690]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623
[]\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 624--624
[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2691]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657
[]\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 661--661
[]\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 668--668
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2692] [2693]
Underfull \hbox (badness 10000) in paragraph at lines 812--813
Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2694]
Underfull \hbox (badness 10000) in paragraph at lines 869--873
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 869--873
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 869--873
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 869--873
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2695]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 900--900
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2696]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2697] [2698]
Underfull \hbox (badness 10000) in paragraph at lines 1076--1077
[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase
/ format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2699] [2700]
Underfull \hbox (badness 10000) in paragraph at lines 1270--1276
[]\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig
n:::writeForeignStata[]\T1/ptm/m/n/10 ,
[2701]
Underfull \hbox (badness 2088) in paragraph at lines 1296--1299
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid
e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET
[2702]) (./lattice-pkg.tex
Chapter 23.
[2703]
Underfull \hbox (badness 2073) in paragraph at lines 117--121
\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
Underfull \hbox (badness 10000) in paragraph at lines 117--121
\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm /
ms / departments / sia /
[2704] [2705]
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"),[]
[2706]
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"),[]
[2707] [2708] [2709] [2710]
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
[2711] [2712] [2713] [2714]
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
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2715]
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 sho
uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2716] [2717]
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
[2718] [2719] [2720]
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 ,
[2721]
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/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 ,
[2722]
Underfull \vbox (badness 10000) has occurred while \output is active [2723]
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
[2724]
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[]\T
1/ptm/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
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
[2725] [2726] [2727] [2728]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
[2729]
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-fie
d, the 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 firs
t checked. If
[2730] [2731] [2732]
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"),[]
[2733] [2734] [2735] [2736] [2737]
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"),[]
[2738] [2739]
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/
pcr/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/ptm/m/n/10 must have the same lengths as
[2740]
Underfull \hbox (badness 6758) in paragraph at lines 2919--2923
[]\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 2919--2923
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra
ster[][][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2925--2927
[]\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][]
[]\T1/ptm/m/n/10 when
Underfull \hbox (badness 1609) in paragraph at lines 2977--2983
[]\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 2977--2983
\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 2977--2983
\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
[2741]
Underfull \hbox (badness 2486) in paragraph at lines 3001--3005
[]\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
[2742]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3104--3104
[] \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 3105--3105
[] \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 3106--3106
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
[2743]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3117--3117
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3129--3129
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2744]
Underfull \hbox (badness 2913) in paragraph at lines 3187--3194
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3187--3194
[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
[2745] [2746] [2747]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3475 \aliasA{parallel}{B\_08\_splom}{parallel}
[2748]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3517--3517
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2749] [2750] [2751] [2752] [2753]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3876--3876
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2754] [2755]
Underfull \hbox (badness 2277) in paragraph at lines 3970--3974
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault
set-tings by
Underfull \hbox (badness 2435) in paragraph at lines 3970--3974
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2756]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4100--4100
[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
Underfull \hbox (badness 1173) in paragraph at lines 4109--4113
[]\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
[2757]
Underfull \hbox (badness 3219) in paragraph at lines 4136--4138
[]\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 4153--4157
[]\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren
t set-tings (ob-tained by
[2758]
Underfull \hbox (badness 5161) in paragraph at lines 4218--4222
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell
is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4218--4222
\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
[2759] [2760]
Underfull \hbox (badness 1067) in paragraph at lines 4336--4346
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/
10 is 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 4336--4346
[]\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 4336--4346
[]\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super
pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4336--4346
[]\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used
only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4336--4346
[]\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/
n/10 col.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 4361--4364
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl
ot.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 4364--4366
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10
plot.polygon []\T1/ptm/m/n/10 and
[2761] [2762] [2763] [2764] [2765]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4768--4768
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2766] [2767]
Underfull \vbox (badness 1092) has occurred while \output is active [2768]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4958
[]\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 .
[2769] [2770]
Underfull \hbox (badness 1442) in paragraph at lines 5087--5090
[]\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle
s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and
[2771] [2772] [2773] [2774] [2775]
Underfull \hbox (badness 3646) in paragraph at lines 5426--5429
[][][]\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-call
y the en-try for
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[] \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 5457--5457
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2776]
Underfull \hbox (badness 10000) in paragraph at lines 5545--5548
[]\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 5545--5548
[]\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the
left of pan-els us-ing
[2777]
Underfull \hbox (badness 1635) in paragraph at lines 5571--5576
[]\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect,
which is to draw a strip ap-pro-pri-ate for
[2778] [2779]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5722--5722
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5736--5736
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5737--5737
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5740--5740
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5743--5743
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
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[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5751--5751
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5752--5752
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5753--5753
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
[2780]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5754--5754
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5755--5755
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5771--5773
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
Underfull \hbox (badness 2376) in paragraph at lines 5782--5784
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2781]
Underfull \hbox (badness 2538) in paragraph at lines 5907--5911
\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul
t 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 5918--5925
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e
x-tra pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5918--5925
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the
se are used (in com-bi-na-tion with
[2782] [2783]
Underfull \hbox (badness 10000) in paragraph at lines 6071--6075
[][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt
ice[][][][]\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 ,
[2784]
Underfull \vbox (badness 10000) has occurred while \output is active [2785]
[2786]
Underfull \hbox (badness 4242) in paragraph at lines 6218--6223
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2787] [2788]
Underfull \hbox (badness 3601) in paragraph at lines 6334--6339
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m
/n/10 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 6334--6339
\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa
ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2789]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6421--6421
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2790] [2791]
Underfull \hbox (badness 1888) in paragraph at lines 6553--6560
[]\T1/pcr/m/n/10 at []\T1/ptm/m/n/10 can be a nu-meric vec-tor, []\T1/pcr/m/n/1
0 col.regions []\T1/ptm/m/n/10 a vec-tor of col-ors, and
[2792]
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[]\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 6610--6613
[]\T1/pcr/m/n/10 shade.colors.palette []\T1/ptm/m/n/10 func-tion should re-turn
a valid color. The
[2793] [2794] [2795] [2796] [2797]
Underfull \hbox (badness 1320) in paragraph at lines 7016--7023
[]\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p
anel func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 7016--7023
\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
[2798] [2799]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7086--7086
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
Underfull \hbox (badness 10000) in paragraph at lines 7116--7120
[]\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 7116--7120
[]\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi
s func-tion is passed
[2800] [2801]
Underfull \hbox (badness 10000) in paragraph at lines 7221--7224
\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
[2802] [2803]
Underfull \hbox (badness 2012) in paragraph at lines 7387--7390
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2804]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7433--7433
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2805] [2806]
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[]\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed o
n to
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[]\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b
e a list of ar-gu-ments to be sup-plied to
[2807]
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[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
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[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2808]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
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[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2809] [2810] [2811]
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[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
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[]\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
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super
pose
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[]\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
[2820] [2821]
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[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
[2822]
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[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
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[]\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
[2823]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2824] [2825]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2826]
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[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2827] [2828]
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[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2829]
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\T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r
ight.x, right.y, left.name, right.x.name,
[2830] [2831] [2832] [2833] [2834] [2835] [2836]
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[]\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1
0 , []\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 ,
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[]\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4
57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 ,
[2837] [2838] [2839]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9923 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2840] [2841] [2842]
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\T1/pcr/m/n/10 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 , []\T1/pcr/m/n/10 He
art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower
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[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2843] [2844]) (./mgcv-pkg.tex
Chapter 24.
[2845] [2846]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
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[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2847]
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[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2848] [2849] [2850] [2851]
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[][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\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 ,
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[][][]\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
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2852]
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2853] [2854] [2855]
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[]\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog"
[]\T1/ptm/m/n/10 and
[2856] [2857]
Underfull \hbox (badness 1406) in paragraph at lines 704--705
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2858] [2859]
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[]\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
[2860]
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[]\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).
[2861]
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[2863] [2864] [2865] [2866] [2867] [2868] [2869]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
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[] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[]
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[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[]
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[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[]
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[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
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[]\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)[]
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[2872]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
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[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
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[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
[2874] [2875] [2876] [2877] [2878] [2879]
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[]\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di
screte=TRUE)[]
[2880] [2881] [2882] [2883]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2884] [2885] [2886] [2887] [2888] [2889] [2890]
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
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[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n
/10 formula.gam[][][] []\T1/ptm/m/n/10 and also
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2891] [2892] [2893]
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\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
[2894] [2895]
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[][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\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
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2896]
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[2900] [2901]
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[]\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1
e-07, maxit = 200,
[2902] [2903] [2904] [2905] [2906] [2907]
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[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
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[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
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[] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU
LL,...)[]
[2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915]
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[]\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
[2916] [2917]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2921] [2922] [2923] [2924] [2925] [2926] [2927]
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[] \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)+[]
[2928] [2929] [2930]
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[]\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0,
d1b = 0,
[2931] [2932]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2933]
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[]\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver-
gence fail-ures, con-sider mod-i-fy-ing
[2934] [2935]
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[][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor
-re-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 ,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n
egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1
0 ,[][][]\T1/pcr/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 .
[2936]
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[2938] [2939] [2940]
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[]\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
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2941] [2942] [2943] [2944] [2945] [2946] [2947]
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(..
.,fit=FALSE) []\T1/ptm/m/n/10 or
[2948] [2949]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
[2950]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
[2951] [2952]
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[] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[]
[2953] [2954] [2955] [2956] [2957]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
[2958]
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[]\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2959] [2960] [2961]
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[2963] [2964]
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[]\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)
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 7373--7373
[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2982] [2983]
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2984] [2985]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[3005]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim
.pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd
Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p
dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 .
[3006]
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[]\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p
dTens[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n
ot nor-mally be
[3007] [3008] [3009]
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[]
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[] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[]
[3010] [3011] [3012]
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[]\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
[3013] [3014] [3015] [3016]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,gc.level=0,...)[]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para-
[3017] [3018] [3019]
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
[3020] [3021]
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[]\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi
nal grid points[]
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[]\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1)
,x3=rep(0,n))[]
[3022]
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[] \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[]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\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
[3025]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
[3026]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al
-though 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,
[3027] [3028] [3029]
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[]\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,
[3030] [3031] [3032] [3033] [3034]
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[]\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
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\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: see
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n
/10 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 10999--11002
\T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s
mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[3035]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[]
[3036]
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[]\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 ,
[3037] [3038] [3039] [3040] [3041]
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[]\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)
[3042] [3043] [3044] [3045] [3046] [3047]
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[] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
+ (eps/del))[]
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[]\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[]
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[3049]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
model ma-trix X, or, if
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[]\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE,
cov = TRUE,[]
[3050]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
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[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
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[]\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
[3054]
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\T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10
vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n
/10 "NA"[]\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w
ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec
[3055]
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[]\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 12225--12229
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc
r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 ,
[3056] [3057] [3058]
Underfull \hbox (badness 6876) in paragraph at lines 12420--12426
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on
e or two vari-ables, spec-i-fied via terms like
[3059]
Underfull \hbox (badness 10000) in paragraph at lines 12461--12462
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3060] [3061]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3062]
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[] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12645--12645
[] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[]
[3063]
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[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
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[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
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[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
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[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[3064]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 12738--12740
\T1/ptm/m/n/10 term []\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
[3065] [3066]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3067] [3068]
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[]\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 12950--12950
[]\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[]
[3069] [3070]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3071] [3072] [3073] [3074] [3075]
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[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3076]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3077] [3078]
Underfull \hbox (badness 10000) in paragraph at lines 13573--13576
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met
hod a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 13573--13576
\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 13573--13576
[]\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"
[3079] [3080]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13659--13659
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3081]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 13704--13710
[]\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-
[3082] [3083] [3084]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13918--13918
[]\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...[]
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[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th
e sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14047--14048
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3087] [3088] [3089]
Underfull \hbox (badness 7613) in paragraph at lines 14192--14195
[]\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [
]\T1/ptm/m/n/10 pro-duced by the
[3090]
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[]\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a
sin-gle smooth-ing pa-ram-e-
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[]\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs
="sz",id=1),data=dat,method="REML")[]
[3091] [3092] [3093]
Underfull \hbox (badness 3396) in paragraph at lines 14405--14408
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an
y num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14450--14452
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3094] [3095] [3096] [3097] [3098] [3099]
Underfull \hbox (badness 10000) in paragraph at lines 14741--14743
[]\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see
Underfull \hbox (badness 10000) in paragraph at lines 14771--14775
[][][]\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 ,
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[][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 soap[][][
][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical.Spline[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14771--14775
[][][]\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 ,
[3100] [3101] [3102] [3103] [3104]
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[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3105] [3106]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15140--15140
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3107] [3108]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 15274--15274
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3109] [3110]
Underfull \hbox (badness 4846) in paragraph at lines 15405--15408
[]\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
[3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121]
[3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130]
Overfull \hbox (120.78088pt too wide) in paragraph at lines 16623--16623
[]\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL,
unconditional=FALSE, ...)[]
[3131]
Underfull \hbox (badness 1715) in paragraph at lines 16645--16646
[]\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object
$Vc []\T1/ptm/m/n/10 (if avail-able) from a
[3132] [3133] [3134]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 16835--16835
[]\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1,
Overfull \hbox (48.78088pt too wide) in paragraph at lines 16837--16837
[]\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16839--16839
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 16859--16860
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 16859--16860
[]\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le
cted by []\T1/pcr/m/n/10 ar.row
[3136]
Underfull \vbox (badness 10000) has occurred while \output is active [3137]
[3138]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17047--17047
[]\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 17048--17048
[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
[3139]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17060--17060
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[3140] [3141] [3142]) (./nlme-pkg.tex
Chapter 25.
[3143]
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
- fit-ted) are used; else, if
[3144]
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
- fit-ted) are used; else, if
[3145] [3146] [3147] [3148] [3149]
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,[]
[3150] [3151]
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 ---------------------------
---------------[]
[3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159]
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"),[]
[3160]
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
.htm[]\T1/ptm/m/n/10 ', the first edi-tion of
[3161] [3162] [3163] [3164] [3165] [3166] [3167]
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.
effects.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
,
[3168]
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
[3169] [3170] [3171] [3172] [3173]
Underfull \hbox (badness 2042) in paragraph at lines 1996--2002
\T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10
group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 ,
[3174]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[3175]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3176] [3177]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR
MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 ,
[3178]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186]
Underfull \hbox (badness 10000) in paragraph at lines 2849--2853
[][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor
Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[
][][][]\T1/ptm/m/n/10 ,
[3187] [3188] [3189] [3190] [3191] [3192pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d
uplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE)
] [3193] [3194] [3195]
[3196] [3197] [3198]
Underfull \hbox (badness 6493) in paragraph at lines 3585--3593
[][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau
s[][][][]\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 corSp
her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T
1/ptm/m/n/10 ,
[3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209]
[3210] [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220]
[3221] [3222]
Underfull \hbox (badness 10000) in paragraph at lines 5165--5169
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p
cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 ,
[3223] [3224] [3225] [3226] [3227] [3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5597--5600
[][][]\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 ,
[3230] [3231] [3232] [3233] [3234] [3235] [3236] [3237] [3238]
Underfull \hbox (badness 2799) in paragraph at lines 6103--6109
\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
[3239]
Underfull \hbox (badness 7133) in paragraph at lines 6164--6168
[]\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 ,
[3240]
Underfull \hbox (badness 2057) in paragraph at lines 6253--6264
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl
sControl[][][][]\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 ,
[3241]
Underfull \hbox (badness 10000) in paragraph at lines 6317--6319
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3242] [3243] [3244] [3245]
Underfull \hbox (badness 7133) in paragraph at lines 6566--6570
[]\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 ,
[3246]
Underfull \hbox (badness 10000) in paragraph at lines 6665--6671
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn
lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6692--6692
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3247]
Underfull \hbox (badness 10000) in paragraph at lines 6730--6732
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3248] [3249] [3250] [3251]
Underfull \hbox (badness 10000) in paragraph at lines 7002--7009
[][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl
y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff
GroupedData[][][][]\T1/ptm/m/n/10 ,
[3252]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7020--7020
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7025--7025
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7047--7049
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr
oupedData []\T1/ptm/m/n/10 ob-ject or a
[3253] [3254] [3255]
Underfull \hbox (badness 10000) in paragraph at lines 7262--7267
[][][]\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 Initi
alize.glsStruct[][][][]\T1/ptm/m/n/10 ,
[3256] [3257] [3258]
Underfull \hbox (badness 1997) in paragraph at lines 7414--7422
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-tion and op-ti-
Underfull \hbox (badness 2205) in paragraph at lines 7414--7422
\T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n
/10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20,
Underfull \hbox (badness 3118) in paragraph at lines 7437--7440
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ
e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/
n/10 ,
[3259] [3260] [3261]
Underfull \hbox (badness 3354) in paragraph at lines 7653--7655
[]\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
[3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269]
Underfull \hbox (badness 10000) in paragraph at lines 8170--8187
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm
e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8170--8187
[][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL
ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\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 8213--8213
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
[3270]
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3271] [3272] [3273] [3274]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8487--8487
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3275]
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[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286]
[3287]
Underfull \hbox (badness 10000) in paragraph at lines 9336--9343
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9347--9347
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3288] [3289] [3290] [3291] [3292]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9698 ...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
<to be read again>
\relax
l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3293]
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[]\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 9762--9765
[]\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 9762--9765
\T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10
. Must have the same di-men-sions as
[3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] [3304]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10442--10442
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3305]
Underfull \hbox (badness 1596) in paragraph at lines 10471--10497
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3306] [3307] [3308]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10647--10647
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3309] [3310]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10798--10798
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10809--10814
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi
nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [
][][]\T1/pcr/m/n/10 nlm[][][]
[3311]
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[]\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p
tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control=
Underfull \hbox (badness 10000) in paragraph at lines 10850--10852
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3312] [3313] [3314] [3315]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11141--11141
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11142--11142
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
[3316] [3317] [3318] [3319] [3320] [3321]
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[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3322] [3323] [3324] [3325] [3326] [3327]
Underfull \hbox (badness 6268) in paragraph at lines 11919--11929
[][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\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[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 ,
[3328] [3329] [3330] [3331]
Underfull \hbox (badness 10000) in paragraph at lines 12180--12186
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 ,
[3332] [3333] [3334] [3335] [3336]
Underfull \hbox (badness 6876) in paragraph at lines 12502--12504
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/
10 ini-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
[3337] [3338]
Underfull \hbox (badness 2452) in paragraph at lines 12658--12665
[][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\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 ,
[3339]
Underfull \hbox (badness 10000) in paragraph at lines 12723--12729
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 ,
[3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13312--13312
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3349] [3350] [3351] [3352] [3353]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13677--13677
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3354]
Underfull \hbox (badness 10000) in paragraph at lines 13704--13707
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3355]
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[]\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 13747--13754
[]\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
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13804--13804
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3356]
Underfull \hbox (badness 10000) in paragraph at lines 13811--13814
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13811--13814
[]\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary
co-vari-ate and a sin-gle
[3357]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped
Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3358] [3359]
Underfull \hbox (badness 10000) in paragraph at lines 14013--14015
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c
ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe
dData[][][][]\T1/ptm/m/n/10 ,
[3360] [3361] [3362] [3363] [3364] [3365] [3366] [3367]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14537--14537
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3368] [3369] [3370] [3371] [3372] [3373] [3374] [3375] [3376]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been
already used, duplicate ignored
<to be read again>
\relax
l.15190 ...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
<to be read again>
\relax
l.15190 ...Extract Random Effects}{random.effects}
[3377] [3378] [3379]
[3380] [3381] [3382] [3383] [3384] [3385] [3386]
Underfull \hbox (badness 2126) in paragraph at lines 15830--15834
[]\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199
7). Phar-ma-coki-net-
[3387]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15838--15838
[]\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15857--15857
[] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718
4, tol = 1.5e-5),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15858--15858
[] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),
tol = 7e-7)[]
[3388]
Underfull \hbox (badness 1009) in paragraph at lines 15888--15897
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3389] [3390]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16035--16035
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3391] [3392] [3393] [3394] [3395]
Underfull \hbox (badness 10000) in paragraph at lines 16370--16376
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l
me[][][][]\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.reStruct[][][][]\T1/ptm/m/n/10 ,
[3396]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16401--16401
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3397] [3398] [3399] [3400] [3401] [3402] [3403]
Underfull \hbox (badness 1728) in paragraph at lines 16889--16892
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3404] [3405] [3406] [3407] [3408]
Underfull \hbox (badness 1803) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite,
Underfull \hbox (badness 10000) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p
dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General
Underfull \hbox (badness 7888) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[
]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object)
[3409]
Underfull \hbox (badness 10000) in paragraph at lines 17294--17295
[]\T1/pcr/m/n/10 "Constant plus power of variance
Underfull \hbox (badness 10000) in paragraph at lines 17295--17296
[]\T1/pcr/m/n/10 "Constant plus proportion of variance
[3410] [3411] [3412] [3413]
Underfull \hbox (badness 10000) in paragraph at lines 17545--17553
[][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo
nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p
tm/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 ,
[3414] [3415] [3416] [3417]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17817--17817
[]\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17819--17819
[]\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[]
[3418] [3419] [3420] [3421] [3422] [3423]
Underfull \hbox (badness 10000) in paragraph at lines 18255--18265
[][][]\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.co
rLin[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18255--18265
[][][]\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 Variogr
am.corSpher[][][][]\T1/ptm/m/n/10 ,
[3424]
Underfull \hbox (badness 3579) in paragraph at lines 18293--18298
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3425]
Underfull \hbox (badness 3579) in paragraph at lines 18357--18362
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3426]
Underfull \hbox (badness 3579) in paragraph at lines 18420--18425
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3427]
Underfull \hbox (badness 1577) in paragraph at lines 18481--18483
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR
atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3428]
Underfull \hbox (badness 3579) in paragraph at lines 18546--18551
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18579--18588
[][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va
riogram[][][][]\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 18579--18588
[][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rRatio[][][][]\T1/ptm/m/n/10 ,
[3429]
Underfull \hbox (badness 3579) in paragraph at lines 18618--18623
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3430] [3431]
Underfull \hbox (badness 1009) in paragraph at lines 18764--18773
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3432] [3433]
Underfull \hbox (badness 1009) in paragraph at lines 18896--18905
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
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\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
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ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
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l.47 ...t Multinomial Log-linear Models}{multinom}
[3443]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3444] [3445] [3446]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3447]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428
[]\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 431--431
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3448] [3449]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3450]) (./rpart-pkg.tex
Chapter 27.
[3451] [3452] [3453] [3454]
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, ...)[]
[3455] [3456] [3457] [3458]
Underfull \hbox (badness 1442) in paragraph at lines 592--598
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil
l be at the hor-i-zon-tal plot co-or-di-nates of
[3459] [3460]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
Underfull \hbox (badness 10000) in paragraph at lines 771--775
[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
adds to the la-bel
Underfull \hbox (badness 1142) in paragraph at lines 771--775
\T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [
]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n
[3461] [3462] [3463]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915
[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
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[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"),[]
[3464] [3465] [3466] [3467]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
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[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
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[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n
/10 rpart []\T1/ptm/m/n/10 al-go-rithm. See
[3468]
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[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\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 1304--1304
[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3469] [3470] [3471] [3472] [3473] [3474] [3475]
Underfull \hbox (badness 1565) in paragraph at lines 1760--1763
[]\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 ',
[3476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1854--1854
[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3477] [3478] [3479]) (./spatial-pkg.tex [3480]
Chapter 28.
[3481] [3482] [3483] [3484] [3485] [3486]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497]
[3498] [3499]) (./survival-pkg.tex [3500]
Chapter 29.
[3501] [3502]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
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[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3503] [3504]
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[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as
long as
[3505] [3506]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again>
\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
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ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
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l.384 ... Myelogenous Leukemia survival data}{aml}
[3507]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
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[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3508]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3509] [3510] [3511]
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[]\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival
[3512]
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3513] [3514]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 935--935
[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3515] [3516] [3517]
Underfull \hbox (badness 1097) in paragraph at lines 1106--1108
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
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[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3518] [3519]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1241--1241
[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3520]
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[]\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter,
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.1308 ...erapy for Stage B/C colon cancer}{colon}
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[] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[]
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[] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[]
[3522] [3523] [3524]
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[] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3525] [3526] [3527] [3528] [3529]
Underfull \hbox (badness 10000) in paragraph at lines 1964--1979
[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
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\T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T
1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe-
Underfull \hbox (badness 10000) in paragraph at lines 1964--1979
\T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv
(time, status) ~ age +
[3530]
Underfull \hbox (badness 3861) in paragraph at lines 2048--2052
[][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][]
[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\
T1/ptm/m/n/10 ,
[3531]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2103--2103
[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3532] [3533] [3534] [3535] [3536] [3537] [3538] [3539]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717
[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3540]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3541] [3542] [3543]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2976--2976
[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3544] [3545] [3546]
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[3548]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3549]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3352--3352
[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
Underfull \hbox (badness 1389) in paragraph at lines 3366--3368
[]\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
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3377--3377
[] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[]
[3550] [3551]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3511--3511
[] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3552] [3553]
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[] []
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[3555]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3556] [3557] [3558] [3559] [3560] [3561] [3562]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4210--4210
[] \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 )))[]
[3563] [3564]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4360--4360
[]\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[]
[3565]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4365--4365
[]\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4369--4369
[]\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2:
4] - yhat[1][]
[3566] [3567]
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[3569] [3570] [3571]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4786--4786
[] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[]
[3572] [3573] [3574]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5016--5016
[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3575] [3576]
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[]\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[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5150--5150
[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3577]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3578]
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[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[]
[3579]
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[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt
m/m/n/10 , which is the re-sult of the
[3580] [3581] [3582]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5512--5512
[]\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1
=FALSE, ...)
[3583]
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[]\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2
), se.fit=TRUE)[]
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[]\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval
ues smooth it.[]
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[]\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g
., svyglm, but[]
[3584]
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[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
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[] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[]
[3585] [3586]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3587]
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[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
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[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
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[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3588] [3589] [3590] [3591] [3592] [3593] [3594]
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[] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[]
[3595] [3596] [3597]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
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[]\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp
"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and
[3598] [3599] [3600] [3601] [3602]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[]
[3603] [3604]
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[]\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE)
[3605]
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[]\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem
ove duplicate times[]
[3606]
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[]\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times=
365*c(3, 5))[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.7224 ...ata from a soldering experiment}{solder}
[3607]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3608] [3609] [3610] [3611] [3612] [3613]
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[]\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[]
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[]\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[]
[3614] [3615] [3616] [3617]
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[] \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 ),[]
[3618] [3619] [3620] [3621]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods
first con-struct a sur-vival curve us-ing
[3622] [3623]
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[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3624] [3625] [3626]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
[3627]
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[]\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre
-dicted sur-vival
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3628]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3629] [3630] [3631] [3632]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10
,
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[] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
ctype,[]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
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[] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2
, ctype,[]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
[3633] [3634] [3635]
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[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3636]
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\T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a-
lent to []\T1/pcr/m/n/10 stype=2,
[3637] [3638]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3639] [3640] [3641] [3642] [3643]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3644]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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[]\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) #
use concordance
[3645] [3646] [3647]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su
rvreg.distributions[][][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T
1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p
tm/m/n/10 ,
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[]\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, i
t is
[3648]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3649]
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[3650] [3651]
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[] \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 )[]
[3652]
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[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
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[] \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 )[]
[3653] [3654] [3655]
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[]\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100
0, data=test)[]
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[]\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[]
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[]\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
set has data[]
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[] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [
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\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p
cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As
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tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel
y anal-o-gously to their
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[][][]\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-l
ar,
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
than 256 (or
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[]\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[]
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[]\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is
true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which
an
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
[42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3406--3406
[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2,
lwd = 1, bty="n")[]
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[]\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
[52]
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[]\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
"", type = "n",[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3446--3446
[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
[53] [54] [55] [56] [57] [58]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[59] [60] [61] [62] [63] [64] [65] [66]
Underfull \hbox (badness 4927) in paragraph at lines 4395--4399
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
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\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 o
r
[67]
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
[68]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[69] [70]
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
[71]
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[72] [73]
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[74] [75] [76] [77]
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[]\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
[78] [79] [80] [81] [82] [83]
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[]\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 []\T1/pcr/m/n/10 c("first",
[84] [85] [86] [87] [88] [89] [90] [91] [92]
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[]\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 : / /
[93] [94] [95]
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\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}[]
[96] [97]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n
/10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\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
[98]
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[]\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
[99] [100]
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
[101]
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[]\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de
fault", "internal",
[102] [103]
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[]\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 ,
[104] [105] [106]
Underfull \hbox (badness 10000) in paragraph at lines 7234--7236
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri
ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n
/10 only. This
Underfull \hbox (badness 6592) in paragraph at lines 7276--7283
\T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http
s : / / specifications . freedesktop .
Underfull \hbox (badness 1735) in paragraph at lines 7276--7283
[]\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion
as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys-
[107] [108]
Underfull \vbox (badness 10000) has occurred while \output is active [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7480--7480
[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[111] [112] [113] [114]
Underfull \hbox (badness 10000) in paragraph at lines 7814--7816
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[115] [116] [117]
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/pcr/m/n/9 ## curlGetHeaders("ftp://cran.r-project.org") ## ftp::// suppo
rt is vanishing[]
[118] [119] [120] [121]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[122]
Underfull \hbox (badness 10000) in paragraph at lines 8322--8332
[]\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 1975) in paragraph at lines 8322--8332
[][][]\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
[123] [124] [125]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8490--8490
[] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[]
[126] [127] [128] [129]
Underfull \hbox (badness 10000) in paragraph at lines 8842--8854
\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 , and
[130] [131] [132] [133] [134] [135]
Underfull \hbox (badness 10000) in paragraph at lines 9291--9295
[]\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions.
Func-tions should be listed in
[136] [137]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9382--9382
[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
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[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9412--9412
[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[138] [139]
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[]\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha
racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b
y
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m
/n/10 formula[][][][]\T1/ptm/m/n/10 s, with
[140] [141] [142]
Underfull \hbox (badness 1603) in paragraph at lines 9794--9797
[]\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
[143] [144] [145] [146] [147] [148] [149] [150] [151]
Underfull \hbox (badness 1917) in paragraph at lines 10410--10415
[]\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10
dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[152]
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[]\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 10466--10466
[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[153] [154]
Underfull \hbox (badness 1168) in paragraph at lines 10568--10573
[]\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\
T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by
[155]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10670--10670
[]\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n
ames(list(...));[]
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[]\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()),
names(list(...))))[]
[156] [157]
Underfull \hbox (badness 2828) in paragraph at lines 10791--10796
[][][]$\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 10791--10796
\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 / IEEE _
Underfull \hbox (badness 10000) in paragraph at lines 10791--10796
\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / /
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[158]
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[]\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[]
[159] [160]
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[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[161] [162] [163]
Underfull \hbox (badness 6396) in paragraph at lines 11242--11250
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
Underfull \hbox (badness 10000) in paragraph at lines 11251--11253
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len
t to but faster than
[164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 11468--11471
[]\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D
LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use
[167] [168] [169] [170] [171] [172]
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[]\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma
y lead to con-fu-sion (see
[173]
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[]\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[]
[174] [175] [176]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1
0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt
m/m/n/10 and
[177]
Underfull \hbox (badness 10000) in paragraph at lines 12246--12249
[]\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used
by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if
Underfull \hbox (badness 10000) in paragraph at lines 12264--12266
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[178] [179] [180] [181]
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc
r/m/n/10 where []\T1/ptm/m/n/10 as
Underfull \hbox (badness 5970) in paragraph at lines 12557--12559
[]\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/10 is true, oth-er-wise
[182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13375--13375
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[194] [195] [196] [197] [198] [199] [200] [201] [202] [203]
Underfull \hbox (badness 2253) in paragraph at lines 14100--14102
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
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[]\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m
a-tion is given about the
[204] [205]
Underfull \hbox (badness 2573) in paragraph at lines 14268--14270
[]\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
[]\T1/pcr/m/n/10 fsep =
[206] [207]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[208] [209]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][][]\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 ,
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[][][]$\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 .
Overfull \hbox (47.58038pt too wide) in paragraph at lines 14580--14580
[] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B
as it exists already[]
[210]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[211]
Underfull \hbox (badness 10000) in paragraph at lines 14702--14705
[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.exists[][][][]\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 14712--14712
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[212]
Underfull \hbox (badness 10000) in paragraph at lines 14778--14781
[]\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d
i-tion ob-ject of class
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14795--14795
[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
[213]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
Underfull \hbox (badness 3965) in paragraph at lines 14856--14860
[]\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,
[214] [215] [216]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15020--15020
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15021--15021
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[217] [218] [219] [220]
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[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
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[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
[221]
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[]\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-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[222]
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[][][]\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/1
0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 ,
[223]
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[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[224] [225]
Underfull \hbox (badness 10000) in paragraph at lines 15612--15614
[]\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p
os-si-bly for-mat-ted) num-bers, also in
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[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
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[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[]
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[]\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
[226]
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[]\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
[227]
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[]\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 ,
which calls []\T1/pcr/m/n/10 .format.zeros(*,
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[]\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call
s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri
des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10
formatC(123.45, mode =
Underfull \hbox (badness 10000) in paragraph at lines 15790--15798
[]\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
[228] [229]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15898--15898
[]\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 ")[]
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[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
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[231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16754--16754
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[242] [243]
Underfull \hbox (badness 2418) in paragraph at lines 16863--16867
\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/pt
m/m/n/10 ,
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s
ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR
UE[]\T1/ptm/m/n/10 , then the sin-gle
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[][][]\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[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][]
\T1/ptm/m/n/10 ,
[244] [245]
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[]\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/
ptm/m/n/10 calls C level
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[]\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose
of flush-ing (i.e., emp-ty-ing) the
[246]
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[]\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f
actory" default[]
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[]\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if
translation works)[]
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[]\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex
ample started:[]
[248] [249]
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[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[250] [251] [252] [253]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17575--17575
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
[254]
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[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 17660--17660
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
[256] [257] [258] [259]
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[]\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)))
[260]
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[]\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[]
[261] [262] [263]
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[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[264] [265] [266] [267] [268]
Underfull \hbox (badness 1163) in paragraph at lines 18653--18655
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 https : / / unicode-[]org . github . io / icu /
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[]\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.[]
[269]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[270]
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[] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se
t = FALSE,[]
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[] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F
ALSE,[]
[271]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
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[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
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[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
[272] [273]
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[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
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[]\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[]
[274] [275] [276]
Underfull \hbox (badness 10000) in paragraph at lines 19194--19196
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T
1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and
[277] [278] [279] [280] [281]
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[282] [283] [284]
Underfull \hbox (badness 4699) in paragraph at lines 19777--19780
[]\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty
pes ([]\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 ,
[285] [286]
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[287] [288] [289]
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[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[290]
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[]\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co
lumn names differ)[]
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[]\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are
not checked)[]
[291] [292] [293] [294] [295] [296] [297] [298] [299]
Underfull \hbox (badness 1975) in paragraph at lines 20709--20712
[]\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
[300] [301] [302] [303] [304] [305]
Underfull \hbox (badness 1077) in paragraph at lines 21124--21129
[]\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st
al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T
1/ptm/m/n/10 and
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[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
[306]
Underfull \hbox (badness 1112) in paragraph at lines 21212--21221
[]\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the
en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 ,
[307]
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[]\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us
ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a
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\T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It
may be opened by
[308] [309]
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[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi
s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no
[]\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m
/n/10 ar-gu-ment, it lists all avail-able pack-
[310] [311]
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[][][]\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 autoloa
d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/
m/n/10 ,
[312]
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[]\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
[313]
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
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\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 21712--21717
\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 21712--21717
\T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s
ion 3 of the li-cense can be dis-played by
[314] [315] [316]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[317]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][] []\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
[318] [319]
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[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
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[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
prob = 0.2))),[]
[320] [321]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
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[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
[322] [323]
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[]\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
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[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
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[]\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war
ning messages[]
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[] \T1/pcr/m/n/9 sg <- matrix(unlist(strsplit(strsplit(Sys.getlocale(), sep)[[
1]], "=")), nrow=2)[]
[324] [325]
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[][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[]
[][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m
/n/10 double[][][] []\T1/ptm/m/n/10 (class
[326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337]
[338]
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[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
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[] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N
aN, imaginary = r ))[]
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[]\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)[]
[339]
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[]\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE
) # |--> "abc"[]
[340]
Underfull \hbox (badness 1655) in paragraph at lines 23554--23558
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[341] [342] [343]
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[]\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 tcross
prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able.
[344] [345] [346] [347] [348] [349] [350] [351] [352]
Underfull \hbox (badness 1484) in paragraph at lines 24392--24400
[]\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 1152) in paragraph at lines 24392--24400
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[353] [354]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24466--24466
[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[355] [356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 1448) in paragraph at lines 25014--25022
[]\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a
s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive =
[363]
Underfull \hbox (badness 3849) in paragraph at lines 25129--25134
[]\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-
nally to a char-ac-ter vec-tor (so meth-ods for
[364]
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[]\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-r
e-spond-ing list,
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\T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\
T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env,
Underfull \hbox (badness 3148) in paragraph at lines 25206--25212
\T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi
-ron-ment is used as a hash ta-ble,
[365] [366] [367]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1
0 c("bytes", "chars",
[368] [369] [370]
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[]\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e
ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by
[371] [372] [373]
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\T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10
and in case of an er-ror (such as in-suf-fi-cient per-
[374] [375] [376] [377]
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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[]\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti
al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use
[378]
Underfull \hbox (badness 2846) in paragraph at lines 26109--26113
[]\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m
ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab
out the pack-
Underfull \hbox (badness 1990) in paragraph at lines 26109--26113
\T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c
om-puted pack-age in-for-ma-tion ob-ject and pass this to
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[]\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only)
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
[379]
Underfull \hbox (badness 10000) in paragraph at lines 26204--26210
[]\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space
it loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 26204--26210
[]\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram
e con-tain-ing the ex-ported val-ues of a
Underfull \hbox (badness 10000) in paragraph at lines 26217--26219
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but
more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in%
[380]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26284--26284
[] \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:[]
[381] [382] [383]
Underfull \hbox (badness 8189) in paragraph at lines 26479--26485
[]\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
[][]mode[][][]
[384] [385] [386]
Underfull \hbox (badness 1694) in paragraph at lines 26704--26707
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[387] [388] [389] [390]
Underfull \hbox (badness 1603) in paragraph at lines 26976--26978
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[391] [392]
Underfull \hbox (badness 1210) in paragraph at lines 27103--27111
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-
[393] [394]
Underfull \hbox (badness 3271) in paragraph at lines 27323--27326
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[395] [396]
Underfull \vbox (badness 3780) has occurred while \output is active [397]
[398]
Underfull \hbox (badness 3138) in paragraph at lines 27629--27635
[]\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 27629--27635
\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 27629--27635
\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 27642--27645
[]\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/pt
m/m/n/10 and
Underfull \hbox (badness 1389) in paragraph at lines 27668--27670
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 (and in-di-rectly
[399]
Underfull \hbox (badness 1009) in paragraph at lines 27728--27731
[]\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p
ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T
1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 27744--27747
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN
ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27752--27758
\T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1
/pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27752--27758
\T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5091) in paragraph at lines 27752--27758
[]\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma
c.binary.universal" []\T1/ptm/m/n/10 are no longer
Underfull \hbox (badness 10000) in paragraph at lines 27767--27774
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][][]\T1/pcr/m/n/10 up
date.packages[][][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 2384) in paragraph at lines 27767--27774
[]\T1/pcr/m/n/10 c(CRAN="@CRAN@")[]\T1/ptm/m/n/10 , a value that causes some ut
il-i-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 27767--27774
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke []\T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 27767--27774
\T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran";
[400] [401] [402] [403] [404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28115--28115
[]\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 28128--28132
[]\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.
y)] = FUN(X[arrayindex.x],
[405] [406]
Underfull \hbox (badness 1210) in paragraph at lines 28275--28278
[]\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la
ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex
t=s,
[407] [408] [409] [410]
Underfull \hbox (badness 7133) in paragraph at lines 28557--28563
[][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc
r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
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[]\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
the longest input.[]
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[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
[411]
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[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling :
[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[]
[412] [413]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28791--28791
[]\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt
cars, cyl == 4))[]
[414]
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[]\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so
is not evaluated[]
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[]\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., []\T1/pcr/m/n/10 type =
[415] [416] [417] [418] [419]
Underfull \hbox (badness 2277) in paragraph at lines 29173--29178
\T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt
m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing
[420] [421]
Underfull \hbox (badness 1701) in paragraph at lines 29289--29293
[]\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/
pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\
T1/pcr/m/n/10 get[][][](name, envir =
[422]
Underfull \hbox (badness 1796) in paragraph at lines 29357--29360
[]\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i
n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed
out-put, see
[423] [424] [425]
Underfull \hbox (badness 10000) in paragraph at lines 29561--29564
[]\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p
rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[426] [427] [428] [429] [430] [431] [432] [433] [434] [435]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 30256--30256
[] \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))[]
[436] [437] [438] [439] [440]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30549--30549
[]\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[]
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[]\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 30566--30566
[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
[441]
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[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v
ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
[442]
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[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
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[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
[443] [444]
Underfull \hbox (badness 3713) in paragraph at lines 30874--30885
[]\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma
n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm
/m/n/10 (not
[445] [446]
Underfull \hbox (badness 1248) in paragraph at lines 31026--31033
\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 31026--31033
\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 /
[447]
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[]\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
[448] [449] [450]
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[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N
A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[451] [452]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31451--31451
[]\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[]
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[]\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
of deparse()[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31455--31455
[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h
ow = "unlist")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31463--31463
[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
[453] [454] [455] [456] [457]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 31771--31771
[]\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl
e prec numbers :[]
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[]\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
# split one double[]
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[]\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31784--31784
[]\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x)
numToBits(x) , raw(64L))[]
Underfull \vbox (badness 10000) has occurred while \output is active [458]
[459]
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[]\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 31879--31884
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
mode:
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\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 ,
[460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 2080) in paragraph at lines 32417--32427
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/
10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n
/10 (ver-sion num-ber, cur-rently 2 or 3),
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[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[468] [469] [470] [471] [472] [473] [474]
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[]\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p
tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 32981--32983
[]\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
[475]
Underfull \hbox (badness 10000) in paragraph at lines 32992--32994
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / /
pubs . opengroup . org / onlinepubs /
Underfull \hbox (badness 1975) in paragraph at lines 32995--32999
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m
/n/10 https : / / www .
[476] [477] [478] [479] [480]
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[]\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete
replications[]
[481]
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[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[482] [483] [484]
Underfull \hbox (badness 2302) in paragraph at lines 33663--33668
[]\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-
ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant
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\T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/
10 round(x, dig -
[485] [486]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
[487] [488] [489] [490] [491] [492] [493]
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[] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob)
&& size <= n/2))[]
[494] [495] [496] [497] [498] [499] [500]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[501]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length
1, it ap-plies to all fields; oth-er-wise, if
[502] [503]
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[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[504] [505] [506] [507]
Underfull \hbox (badness 4752) in paragraph at lines 35241--35244
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/
m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 5563) in paragraph at lines 35245--35251
[]\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
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517]
Underfull \hbox (badness 10000) in paragraph at lines 35915--35926
[]\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a
p-pli-ca-tion as well as
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\T1/ptm/m/n/10 the shell. It may de-pend on the com-piler used: Mi-crosoft's ru
les for the C run-
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\T1/ptm/m/n/10 time are given at [][]$\T1/pcr/m/n/10 https : / / docs . microso
ft . com / en-[]us / cpp / c-[]language /
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\T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][
]\T1/ptm/m/n/10 . It may de-pend on the
[518] [519] [520] [521] [522] [523] [524] [525]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 36455--36455
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[526] [527] [528]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36707--36707
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
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[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[529]
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[][][]\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[][][]()[]\T
1/ptm/m/n/10 , see also
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[][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \
T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[530] [531]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36863--36863
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[532] [533] [534] [535] [536]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37206--37206
[]\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)[]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[537] [538] [539]
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[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
[540] [541] [542]
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[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
Overfull \hbox (12.78088pt too wide) in paragraph at lines 37674--37674
[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[543] [544] [545] [546] [547]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 38005--38005
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[548]
Underfull \hbox (badness 6110) in paragraph at lines 38101--38111
[]\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-at
e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 38101--38111
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
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\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert
a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 38101--38111
\T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages
on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 38101--38111
\T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as
an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ).
Us-ing
[549]
Underfull \hbox (badness 10000) in paragraph at lines 38157--38163
[]\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 38157--38163
\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,
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\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 1460) in paragraph at lines 38172--38179
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 38172--38179
\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 38172--38179
\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
[550]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38234--38234
[]\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba
ckslashes in[]
[551] [552] [553]
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[]\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T
1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
[554] [555] [556] [557] [558] [559] [560]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 38955--38955
[]\T1/pcr/m/n/9 (fF <- format(.POSIXct(notF))) # was all NA, now the last is
still NA (not "NA")[]
[561] [562]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 39064--39064
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[563] [564] [565]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[566]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[567] [568] [569] [570] [571] [572] [573]
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[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
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[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
[574]
Underfull \hbox (badness 10000) in paragraph at lines 39859--39866
[]\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 39859--39866
[]\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form
at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m
/n/10 ).
[575]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39912--39912
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[576] [577] [578] [579]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 40223--40223
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[580] [581] [582]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 40389--40389
[]\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.
[583]
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[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
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[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 40457--40463
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call.
Underfull \hbox (badness 4792) in paragraph at lines 40476--40481
[]\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10
this may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 40476--40481
[]\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
[584] [585] [586] [587]
Underfull \hbox (badness 10000) in paragraph at lines 40764--40768
[]\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent
s []\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
[588]
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[]\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy
s.function []\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
[589] [590]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 40917--40917
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[591]
Overfull \hbox (19.22812pt too wide) in paragraph at lines 40998--40998
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used
[592] [593]
Underfull \hbox (badness 1082) in paragraph at lines 41143--41146
[]\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions
keep their source in-clud-ing com-ments, see
[594]
Underfull \hbox (badness 10000) in paragraph at lines 41170--41172
[][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo
adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li
brary[][][](.) []\T1/ptm/m/n/10 and uses
[595] [596]
Underfull \hbox (badness 1038) in paragraph at lines 41336--41339
[]\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c
at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[597] [598] [599] [600] [601]
Underfull \hbox (badness 1442) in paragraph at lines 41701--41705
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout
= TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout =
[602] [603] [604] [605]
Underfull \hbox (badness 4096) in paragraph at lines 41955--41958
[]\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri
nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin.
table[][][][]\T1/ptm/m/n/10 ,
[606]
Underfull \hbox (badness 7888) in paragraph at lines 42069--42073
[]\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can
have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/
m/n/10 length(bin) >
[607] [608] [609]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 42223--42223
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (30.0281pt too wide) in paragraph at lines 42225--42225
[] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[]
Overfull \hbox (55.67578pt too wide) in paragraph at lines 42227--42227
[] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 =
NULL), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 42240--42242
[]\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t
hat was reg-is-tered ear-lier via
[610]
Underfull \hbox (badness 10000) in paragraph at lines 42320--42323
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[611] [612]
Underfull \hbox (badness 3872) in paragraph at lines 42438--42441
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 5475) in paragraph at lines 42504--42508
[][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback
Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[614] [615] [616] [617] [618] [619]
Underfull \hbox (badness 1655) in paragraph at lines 42927--42934
\T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[]
\T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1
/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ',
Underfull \hbox (badness 2253) in paragraph at lines 42935--42940
[]\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se
e the ex-am-ples for typ-i-cal cases. It may
Underfull \hbox (badness 1655) in paragraph at lines 42935--42940
\T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 ,
some-thing like `[]\T1/pcr/m/n/10 "2020a"[]\T1/ptm/m/n/10 '. (It does on sys-te
ms us-ing
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[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-
turns the time-zone names known to the cur-rently se-
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\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
[620]
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[]\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/1
0 ' in that di-rec-tory states the ver-sion. That op-tion is
[621]
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\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
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[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
[622]
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[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[623] [624] [625] [626]
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[]\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[]
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[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
[627]
Underfull \vbox (badness 10000) has occurred while \output is active [628]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 43602--43602
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
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[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
[629] [630] [631] [632]
Underfull \hbox (badness 6542) in paragraph at lines 43878--43880
[]\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 , an
d
[633]
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
[634]
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[]\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any
er-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 44065--44073
\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
[635]
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[][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle
rs and sup-press-ing the print-ing of er-ror mes-sages;
[636]
Underfull \hbox (badness 3895) in paragraph at lines 44167--44179
[]\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 44167--44179
\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 ,
[637] [638] [639] [640] [641]
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[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[642] [643] [644] [645] [646] [647]
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[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
[648]
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[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[]
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[][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc
ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n
/10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][]
\T1/ptm/m/n/10 ,
[649]
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[][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di
r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/
ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\
T1/ptm/m/n/10 ,
[650]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 45136--45136
[]\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[]
[651]
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[]\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\
T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ),
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[]\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
[652] [653] [654]
Underfull \hbox (badness 3668) in paragraph at lines 45432--45434
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[655]
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[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[656] [657]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 45613--45613
[]\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 45621--45621
[]\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
There were 105 warnings ...[]
[658]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 45715--45715
[]\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[]
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[]\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings
AsFactors = FALSE) {[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 45720--45720
[] \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa
ctors=stringsAsFactors)[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix
- dropping time info {sec,min,hour, isdst}[]
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[]\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[]
[659]
Underfull \hbox (badness 10000) in paragraph at lines 45791--45796
[]\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 2564) in paragraph at lines 45791--45796
[]\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name
ly a ma-trix whose rows each
[660] [661]
Underfull \hbox (badness 2818) in paragraph at lines 45887--45893
[]\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 and []\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
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45922--45922
[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[662] [663] [664] [665] [666] [667] [668]
Underfull \hbox (badness 2846) in paragraph at lines 46381--46385
[]\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren
tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[669]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 46421--46421
[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
Underfull \hbox (badness 3209) in paragraph at lines 46442--46446
[]\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da
rd' reg-exps, in-clud-ing el-e-ments named
[670]) (./compiler-pkg.tex
Chapter 2.
[671]
Underfull \hbox (badness 2884) in paragraph at lines 106--120
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b
e used to con-trol com-piler op-er-a-tion. There are cur-
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\T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef
ined[]\T1/ptm/m/n/10 , and
[672] [673] [674]) (./datasets-pkg.tex
Chapter 3.
[675] [676] [677] [678] [679]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301
[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[680]
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[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
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[682] [683] [684]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617
[] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[]
[685]
Underfull \hbox (badness 4779) in paragraph at lines 704--707
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[686] [687]
Underfull \hbox (badness 4779) in paragraph at lines 837--840
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[688] [689] [690]
Underfull \hbox (badness 1097) in paragraph at lines 1037--1041
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[691]
Underfull \hbox (badness 4779) in paragraph at lines 1152--1155
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[692] [693] [694] [695] [696]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464
[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[697] [698]
Underfull \hbox (badness 10000) in paragraph at lines 1549--1552
[]\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr
ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q
uarterly.revenue[]\T1/ptm/m/n/10 ,
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[]\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-taine
d from the above
[699] [700] [701]
Underfull \hbox (badness 4779) in paragraph at lines 1738--1741
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[702]
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[]\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 1840--1840
[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[703] [704]
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[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957
[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[705] [706] [707] [708]
Underfull \hbox (badness 4779) in paragraph at lines 2160--2163
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[709] [710] [711]
Overfull \vbox (4.29591pt too high) has occurred while \output is active
[712] [713] [714] [715] [716]
Underfull \hbox (badness 4779) in paragraph at lines 2725--2728
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[717]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[718]
Underfull \vbox (badness 2376) has occurred while \output is active [719]
[720] [721] [722] [723]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[724] [725] [726] [727] [728] [729] [730] [731]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3611--3611
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[732] [733]
Underfull \hbox (badness 4779) in paragraph at lines 3759--3762
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[734]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[735]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[736]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
Underfull \hbox (badness 10000) in paragraph at lines 4006--4008
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
Underfull \hbox (badness 10000) in paragraph at lines 4006--4008
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750]) (./grDevices-pkg.tex
Chapter 4.
[751] [752] [753] [754]
Underfull \hbox (badness 4752) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/
ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p
tm/m/n/10 in
[755] [756] [757] [758]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[759] [760] [761] [762] [763] [764] [765] [766] [767] [768]
Underfull \hbox (badness 5175) in paragraph at lines 1192--1194
[]\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
[769] [770] [771]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363
[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[772] [773] [774]
Underfull \hbox (badness 3302) in paragraph at lines 1624--1628
[]\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo
re of
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[]\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern")
[775] [776] [777] [778] [779]
Underfull \hbox (badness 1565) in paragraph at lines 1914--1919
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i
s to pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1914--1919
\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
[780]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[781]
Underfull \hbox (badness 1184) in paragraph at lines 2038--2048
[]\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 2038--2048
[]\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp
ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 ,
[782]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[783] [784] [785]
Underfull \hbox (badness 6758) in paragraph at lines 2329--2332
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[786] [787]
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[]\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se
tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place
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\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
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\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 2447--2457
[]\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10
setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics
[788]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[789] [790]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2666--2666
[]\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2667--2667
[]\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[]
[791] [792] [793] [794]
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Underfull \vbox (badness 10000) has occurred while \output is active [795]
[796] [797] [798] [799]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3273--3273
[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[800]
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[]\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 3358--3358
[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[801] [802] [803]
Underfull \hbox (badness 10000) in paragraph at lines 3516--3522
[]\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b
ased on the inter-quartile range
[804]
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[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[]
[805]
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[]\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[]
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[]\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[]
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[] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab =
"", main=main)[]
[806]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
[807]
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[]\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 ,
[808]
Underfull \hbox (badness 2189) in paragraph at lines 3848--3853
[]\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work
s well for shad-ing points or lines in up to five groups,
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[809]
Underfull \vbox (badness 10000) has occurred while \output is active [810]
Underfull \hbox (badness 5260) in paragraph at lines 4016--4019
[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10
give a C in-te-ger for-mat such as
[811] [812] [813] [814] [815]
Underfull \hbox (badness 5939) in paragraph at lines 4349--4354
[]\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 family[]\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 ,
[816] [817] [818] [819] [820] [821] [822] [823]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4869--4869
[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[824] [825]
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[826]
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
Underfull \hbox (badness 7522) in paragraph at lines 5139--5145
[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10
give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as
[827]
Underfull \hbox (badness 1112) in paragraph at lines 5172--5176
[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), []\T1/pcr/m/n/10 "CP1251.enc"
[828]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[829] [830] [831]
Underfull \hbox (badness 7344) in paragraph at lines 5494--5496
[]\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 5505--5509
[][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][]
[]\T1/ptm/m/n/10 which is called from both
[832] [833]
Underfull \hbox (badness 1552) in paragraph at lines 5632--5641
[]\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 "He
lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal
atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc
r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\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/p
cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2221) in paragraph at lines 5642--5644
[]\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and
Underfull \hbox (badness 4686) in paragraph at lines 5674--5680
[]\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p
cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for
[834]
Underfull \hbox (badness 5388) in paragraph at lines 5700--5702
[]\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p
cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
[835] [836]
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[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[837]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
[838] [839]
Underfull \hbox (badness 10000) in paragraph at lines 6001--6003
[]\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][]
\T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T
1/ptm/m/n/10 for on-screen de-vices and to
[840] [841] [842] [843] [844]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6368--6368
[]\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 6382--6385
[]\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r
ed/green/blue) into HSV space
[845] [846] [847] [848] [849] [850]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6717--6717
[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6724--6724
[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
[851] [852] [853] [854]
Underfull \hbox (badness 10000) in paragraph at lines 6990--6995
[]\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 pointsize[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/
ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi
rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
fillOddEven []\T1/ptm/m/n/10 and
[855]
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[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
[856]
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[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 2393) in paragraph at lines 7135--7138
\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
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[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
[857]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[858]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ
K lan-guages and
[859]
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of []
\T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu
x sys-tems which have the Wine
[860]
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[]\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d
o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and
[861]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[862] [863]
Underfull \hbox (badness 5637) in paragraph at lines 7630--7636
[]\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
,
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[]\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 /
[864] [865] [866]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10
number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of
[867] [868]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 4647) 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 []\T1/pcr/m/n/10 library(help =
[869] [870] [871] [872] [873] [874] [875]
Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450
[] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[]
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[]\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
[876] [877]
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[]\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[]
[878]
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[]\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 694--698
[][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T
1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\
T1/ptm/m/n/10 if
[879] [880]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 770--770
[]\T1/pcr/m/n/9 ## 1e-01 1e+01 1e+03 1e+05 1e+07 1e+09 1e+11 ; since R 4.2.0:
1e-2 1e0 1e2 .. 1e10[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 782--782
[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 819--819
[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
[881] [882] [883]
Underfull \hbox (badness 10000) in paragraph at lines 966--970
[][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1
/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl
e.
Overfull \hbox (133.98029pt too wide) in paragraph at lines 983--983
[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 985--985
[]\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset
= Age=="Adult"))[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 987--987
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
[884] [885] [886] [887]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1271--1271
[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
[888] [889] [890]
Underfull \hbox (badness 2503) in paragraph at lines 1433--1442
\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and
[]\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt
m/m/n/10 ),
[891] [892]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1542--1542
[]\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 1543--1543
[]\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 1549--1549
[]\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 1550--1550
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[893] [894] [895] [896] [897]
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[][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr
/m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and
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[]\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[]
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[]\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[]
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
[898] [899]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[900] [901]
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[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[]
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[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
[902] [903]
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[]\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8,
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[] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[]
[904]
Underfull \hbox (badness 1430) in paragraph at lines 2335--2337
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10
"n" []\T1/ptm/m/n/10 to sup-press and see also
[905]
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[] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[]
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\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
[906]
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[][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p
tm/m/n/10 and
[907] [908] [909] [910]
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[911]
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[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[912] [913]
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\T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1
/pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy
[914]
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[]\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 :[]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[915]
Underfull \hbox (badness 10000) in paragraph at lines 3042--3045
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1
/pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as
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[]\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w
rong" message:[]
[916] [917] [918]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3257--3257
[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
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[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[919] [920]
Underfull \hbox (badness 10000) in paragraph at lines 3404--3409
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f
ied, raster im-ages are used when the
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[][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true,
the grid is reg-u-lar and ei-ther
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[][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt
m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is
[921] [922] [923]
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[924] [925] [926]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3798--3798
[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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[] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l
engths & coords[]
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[] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3844--3844
[] \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 [927]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3870--3870
[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc
r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3872--3872
[]\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow
(VADeaths)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3883--3883
[]\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7
, lty = 1:7,[]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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Overfull \hbox (42.18039pt too wide) in paragraph at lines 3906--3906
[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
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[]\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset
= .02",inset = .02)[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3916--3916
[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3926--3926
[]\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized"
, "columns."),[]
[929]
Underfull \hbox (badness 10000) in paragraph at lines 3988--3992
[][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth
od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\
T1/pcr/m/n/10 type %in%
[930]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4100--4100
[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[931] [932] [933]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4254--4254
[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
[934]
Underfull \hbox (badness 3930) in paragraph at lines 4333--4335
[]\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
[935] [936] [937] [938] [939]
Underfull \hbox (badness 1286) in paragraph at lines 4644--4647
[]\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 3229) in paragraph at lines 4652--4657
[]\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
[940] [941]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4748--4748
[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor,[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
[942]
Underfull \hbox (badness 1264) in paragraph at lines 4944--4957
\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/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 axis[][][][]\T1/ptm/m/n/10 ,
[943] [944] [945] [946]
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[947 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//mai.pdf>]
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[948 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//oma.pdf>]
[949] [950]
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[]\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 5518--5518
[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[952] [953] [954] [955] [956]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5883--5883
[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
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[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
[957]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again>
\relax
l.5943 \aliasA{plot}{plot.default}{plot}
[958] [959] [960] [961] [962]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6275--6275
[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[963] [964]
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[] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co
llapse = "\n")),[]
[965] [966] [967] [968]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[969] [970]
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[]\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
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[][]
[971 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//pch.pdf>]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
[972]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[974]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[975]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T
1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or
[976] [977] [978] [979]
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[980] [981] [982] [983] [984] [985]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
[986]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[987] [988] [989] [990] [991]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[992] [993] [994]
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[]\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)
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[]\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)[]
[995] [996]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
[997]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh
tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 )
is drawn. For
[998]
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[]
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
lambda = 2),[]
[999] [1000]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[1001] [1002]
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[] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile:
Règles, Liberté, Egalité, Fraternité...")[]
[1003]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m
/n/10 par(c("font.sub",
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[]\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 a
re []\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
[1004]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again>
\relax
l.9018 \HeaderA{units}{Graphical Units}{units}
[1005]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[1006] [1007]
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[]\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)[]
[1008]) (./grid-pkg.tex
Chapter 6.
[1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018]
Underfull \hbox (badness 4859) in paragraph at lines 634--637
[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
to the
[1019] [1020] [1021] [1022] [1023] [1024]
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
[1025] [1026] [1027]
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[] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
[1028] [1029] [1030] [1031]
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[]\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
[1032] [1033] [1034] [1035] [1036] [1037] [1038]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[1039] [1040] [1041]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[]
[1042]
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[]\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 ,
[1043]
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[]\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
[1044] [1045] [1046]
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[]\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
[1047] [1048] [1049]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
[1050]
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
[1051] [1052]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
[1053]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[1054] [1055]
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[]\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix;
see
[1056] [1057] [1058]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[1059] [1060] [1061] [1062] [1063]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1064] [1065]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just=
c("left", "bottom")))[]
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[]\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa
ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see
[1066] [1067]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
[1068] [1069] [1070]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
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[]\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[]
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[1083]
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[]\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
[1084] [1085] [1086] [1087]
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
[1088] [1089]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1090] [1091] [1092] [1093] [1094] [1095]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve
c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list
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\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For
[]\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther
[1096] [1097]
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[]\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob
-ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a
[1098] [1099] [1100]
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a
r-gu-ments above are passed to
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[1112] [1113] [1114] [1115] [1116] [1117]
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
[1118]
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[]\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip()
, device=TRUE)
[1119] [1120]
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[]\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
[1121]
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[][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push
Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 ,
[1122] [1123] [1124] [1125] [1126]
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
[1127]) (./methods-pkg.tex [1128]
Chapter 7.
[1129] [1130]
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[]\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how
co-erce meth-ods work. Use
[1131] [1132] [1133]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in-
for-ma-tion about group generic func-tions; [][]Meth-
[1134] [1135]
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[]\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall
y a primitive.[]
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[]\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[]
[1136]
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[]\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[]
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[]\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[]
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[]\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b
y callNextMethod[]
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[]\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
"B0" method[]
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[]\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[
]
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[1150] [1151] [1152]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
[1153] [1154]
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[]\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/
10 can be an ob-ject of class
[1155] [1156] [1157]
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[]\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 =
[1158] [1159]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment
[][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
[1160] [1161] [1162]
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[]\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\
T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c
re-ate ob-jects of class
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[]\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
[1163]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1164] [1165] [1166]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1167] [1168] [1169] [1170] [1171] [1172] [1173]
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[]\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r
e-turns the im-plicit generic ver-sion,
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[]\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici
t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents
[1174] [1175]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10
getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class
[1176]
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[]
[1177] [1178]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit
ude =
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
[1179]
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,
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[]\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
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[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
[1186]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1187] [1188] [1189]
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[]\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 ,
[1190] [1191] [1192]
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[]\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
[1193] [1194] [1195] [1196]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1197]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[1199]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1200] [1201]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1202] [1203] [1204]
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[]\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
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p
tm/m/n/10 is equiv-a-lent to in-vok-ing the method
[1211] [1212]
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T
1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions,
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\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
[1213]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1214] [1215]
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][][]\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
[1216]
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[1218] [1219]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6981 \aliasA{S4}{S3Part}{S4}
[1220]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
[1221] [1222]
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[]\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
datasets::iris)[]
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[]\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[]
[1223]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again>
\relax
l.7237 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
ignored
<to be read again>
\relax
l.7239 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again>
\relax
l.7240 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.7242 \aliasA{Ops}{S4groupGeneric}{Ops}
pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7243 \aliasA{Summary}{S4groupGeneric}{Summary}
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[]\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
[1224]
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[]\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p
tm/m/n/10 , []\T1/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 ,
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[]\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p
tm/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 "c
os"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7317--7329
[]\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp
i"[]\T1/ptm/m/n/10 ,
[1225] [1226]
Underfull \hbox (badness 1694) in paragraph at lines 7480--7482
[]\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 7504--7507
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS
uperClasses() []\T1/ptm/m/n/10 which calls
[1227]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7525--7525
[]\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[]
[1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238]
[1239] [1240]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1241]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1242] [1243] [1244] [1245]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1246] [1247] [1248]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1249] [1250] [1251]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9437--9437
[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
[1252] [1253] [1254] [1255]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1256]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9866--9866
[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
Underfull \hbox (badness 10000) in paragraph at lines 10564--10566
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi
on" []\T1/ptm/m/n/10 for class
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[]\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 10572--10576
[]\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10
"function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1267] [1268] [1269]) (./parallel-pkg.tex [1270]
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/p
cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][]
RNG[][][]: see
[1271]
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[]\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a
nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for
[1272] [1273]
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[]\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
[1274]
Underfull \hbox (badness 1320) in paragraph at lines 301--304
[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD,
So-laris and Win-dows.
[1275] [1276]
Underfull \hbox (badness 10000) in paragraph at lines 445--447
[]\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
[1277] [1278] [1279] [1280] [1281]
Underfull \hbox (badness 1917) in paragraph at lines 779--788
[]\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 779--788
[]\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe
s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If
[1282] [1283]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 872--872
[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1284] [1285] [1286]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1067--1067
[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1287]
Underfull \hbox (badness 5388) in paragraph at lines 1182--1187
[]\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
[1288]
Underfull \hbox (badness 10000) in paragraph at lines 1206--1214
[]\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 1243--1243
[]\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)[]
[1289] [1290]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1359--1359
[] \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 1373--1373
[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
[1291]
Underfull \hbox (badness 1577) in paragraph at lines 1402--1405
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10
.Random.seed []\T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1449--1451
[]\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
[1292] [1293]) (./splines-pkg.tex [1294]
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 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1303]
Underfull \hbox (badness 1043) in paragraph at lines 597--599
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec
t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the
[1304] [1305]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 712--712
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1306] [1307] [1308]) (./stats-pkg.tex
Chapter 10.
[1309]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\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"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
[]\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
Species" with 3 levels:[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94
[] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
list, as no factors[]
[1310] [1311] [1312] [1313] [1314]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445
[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
[1315]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468
[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1316] [1317] [1318] [1319] [1320] [1321]
Underfull \hbox (badness 1024) in paragraph at lines 887--889
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l
m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for
[1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1625--1625
[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1628--1628
[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
[1333] [1334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1775--1775
[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
[1335]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1787--1787
[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
]
[1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346]
[1347] [1348] [1349]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2805--2805
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1350] [1351] [1352] [1353]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3053--3053
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1354] [1355] [1356]
Underfull \hbox (badness 10000) in paragraph at lines 3264--3266
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo
geneity of
[1357]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3313--3313
[]\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 3314--3314
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1358] [1359] [1360] [1361]
Package amsmath Warning: Foreign command \atopwithdelims;
(amsmath) \frac or \genfrac should be used instead
(amsmath) on input line 3642.
[1362]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3708--3708
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1363] [1364] [1365] [1366]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3987--3987
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1367] [1368] [1369] [1370] [1371]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4276--4276
[]\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 4277--4277
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1372] [1373] [1374] [1375]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4518--4518
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1376] [1377]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4693--4693
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1378] [1379]
Underfull \hbox (badness 3989) in paragraph at lines 4787--4794
[]\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 =
[1380] [1381] [1382] [1383] [1384]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5172--5172
[]\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 5174--5174
[]\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))[]
[1385] [1386] [1387]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5396--5396
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
[1388] [1389] [1390] [1391]
Underfull \hbox (badness 1436) in paragraph at lines 5624--5629
[]\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 5624--5629
\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 5624--5629
\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 ,
[1392] [1393] [1394]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5827--5827
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1395] [1396]
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[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1397] [1398] [1399]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6179--6179
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1400] [1401]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6287--6287
[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
[1402] [1403] [1404] [1405]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1406]
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[]\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca
n 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 6636--6638
[]\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g
ram []\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 6639--6644
\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,
[1407]
Underfull \hbox (badness 7238) in paragraph at lines 6675--6678
[][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti
on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend
rogram[][][] []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[]
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[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
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[]\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):[]
[1408]
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[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
[1409] [1410] [1411]
Underfull \vbox (badness 10000) has occurred while \output is active [1412]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6994--6994
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1413] [1414]
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[1416] [1417] [1418]
Underfull \hbox (badness 10000) in paragraph at lines 7394--7398
[]\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 "bi
nary" []\T1/ptm/m/n/10 or
[1419]
Underfull \hbox (badness 6493) in paragraph at lines 7493--7496
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][]
\T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the
[1420] [1421]
Underfull \hbox (badness 10000) in paragraph at lines 7630--7633
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427]
Underfull \hbox (badness 10000) in paragraph at lines 8042--8047
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences []
\T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 ,
...,
[1428] [1429] [1430] [1431] [1432] [1433]
Underfull \hbox (badness 1210) in paragraph at lines 8397--8399
[]\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al
so be sup-plied as named ar-gu-ments to
[1434] [1435] [1436] [1437] [1438] [1439]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8860--8860
[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
[1440]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8905--8905
[]\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 8908--8908
[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9488--9488
[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9489--9489
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
[1449] [1450] [1451]
Underfull \hbox (badness 7291) in paragraph at lines 9668--9670
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test
of homogeneity of
[1452] [1453] [1454] [1455] [1456] [1457] [1458]
Underfull \hbox (badness 6944) in paragraph at lines 10160--10166
[][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in-
ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment
);
[1459] [1460] [1461]
Underfull \hbox (badness 3758) in paragraph at lines 10374--10377
[]\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
[1462] [1463] [1464] [1465]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10618--10618
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
Underfull \hbox (badness 4518) in paragraph at lines 10644--10649
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1466]
Underfull \hbox (badness 4132) in paragraph at lines 10683--10687
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
Underfull \hbox (badness 1112) in paragraph at lines 10737--10743
[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second
[]\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 10788--10791
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic
ients[][][][]\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
[1468] [1469] [1470]
Underfull \hbox (badness 2142) in paragraph at lines 11005--11008
[]\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 ^^@
[1471]
Underfull \hbox (badness 1708) in paragraph at lines 11086--11090
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1472]
Underfull \hbox (badness 10000) in paragraph at lines 11128--11134
[][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1
0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1
0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11166--11171
[]\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui
tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (=
[1473] [1474]
Underfull \hbox (badness 2635) in paragraph at lines 11299--11302
\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/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 )
meth-ods and the
[1475] [1476] [1477]
Underfull \hbox (badness 1694) in paragraph at lines 11482--11485
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1478]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11580--11580
[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
[1479]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11613--11613
[] \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 11626--11630
[]\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\
T1/ptm/m/n/10 (the de-fault) or
[1480] [1481] [1482] [1483] [1484]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11948--11948
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
[1485]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again>
\relax
l.11963 \aliasA{hat}{influence.measures}{hat}
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12023--12023
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
[1486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12035--12035
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
Underfull \hbox (badness 1062) in paragraph at lines 12088--12093
[]\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me
nts are there to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12105--12107
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists
mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1487] [1488] [1489] [1490]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12360--12360
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12361--12361
[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 10000) in paragraph at lines 12707--12709
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de
fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12730--12732
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 3417) in paragraph at lines 13037--13039
[]\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 []\T1/pcr/m/n/10 ob <-
Underfull \hbox (badness 2894) in paragraph at lines 13043--13047
[]\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 13043--13047
\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti
ve (or true), trac-ing in-for-ma-tion on the
[1502] [1503] [1504] [1505] [1506] [1507]
Underfull \hbox (badness 1496) in paragraph at lines 13457--13463
[]\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran-
dom-iza-tion Dis-tri-bu-tions of
[1508] [1509] [1510] [1511]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13706--13706
[]\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[]
[1512]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13807--13807
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1513]
Underfull \hbox (badness 4518) in paragraph at lines 13855--13860
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516]
Underfull \hbox (badness 10000) in paragraph at lines 14062--14066
[]\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava
il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][]
[]\T1/ptm/m/n/10 ,
[1517] [1518] [1519] [1520] [1521]
Underfull \hbox (badness 1163) in paragraph at lines 14402--14410
\T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc
on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re
siduals[][][][]\T1/ptm/m/n/10 ,
[1522] [1523]
Underfull \hbox (badness 4518) in paragraph at lines 14522--14527
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1524] [1525] [1526]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14710--14710
[]\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 14711--14711
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1527] [1528] [1529] [1530] [1531]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15054--15054
[]\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 15055--15055
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1532]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 15148--15148
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1533] [1534] [1535] [1536] [1537] [1538] [1539]
Underfull \hbox (badness 2726) in paragraph at lines 15557--15560
[]\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [
]\T1/pcr/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 ,
[1540]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15651--15651
[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
[1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 16278--16278
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1551] [1552]
Underfull \hbox (badness 1490) in paragraph at lines 16425--16430
\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
[1553]
Underfull \hbox (badness 1648) in paragraph at lines 16491--16493
[]\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,
[1554]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16576--16576
[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16577--16577
[]\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[]
[1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17134--17134
[]\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[]
[1564] [1565] [1566]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17366--17366
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576]
Underfull \vbox (badness 10000) has occurred while \output is active [1577]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 18088--18088
[]\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
Underfull \vbox (badness 10000) has occurred while \output is active [1578]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 18106--18106
[]\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n
umerical differentiation,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 18107--18107
[]\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo
w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 18111--18111
[]\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co
nverging on *some*):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18112--18112
[]\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal
ler than above[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 18115--18115
[] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl
("^NixOS", osVersion)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18147--18147
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1579] [1580] [1581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18323--18323
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
[1582]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18370--18370
[]\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 18417--18417
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1583] [1584] [1585] [1586]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 18623--18623
[] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[]
[1587] [1588] [1589] [1590] [1591]
Underfull \hbox (badness 1248) in paragraph at lines 18938--18941
[]\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 1661) in paragraph at lines 18951--18955
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18959--18963
\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
[1592]
Underfull \hbox (badness 2042) in paragraph at lines 19017--19019
[]\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
[1593]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 19123--19123
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
[1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19166--19166
[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19184--19184
[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19187--19187
[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19207--19207
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
[1595]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19210--19210
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
Underfull \hbox (badness 2564) in paragraph at lines 19245--19256
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva
l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m
/n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/
10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19245--19256
\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
[1596]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19308--19308
[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1597] [1598] [1599]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19535--19535
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1600] [1601]
Underfull \hbox (badness 1337) in paragraph at lines 19646--19649
[]\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
[1602] [1603] [1604] [1605] [1606]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19965--19965
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1607] [1608]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 20053--20053
[] \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 (12.78088pt too wide) in paragraph at lines 20055--20055
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20057--20057
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1609]
Underfull \hbox (badness 10000) in paragraph at lines 20117--20123
\T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di
stance", lty = cook.lty,
Underfull \hbox (badness 10000) in paragraph at lines 20117--20123
\T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp
Underfull \hbox (badness 10000) in paragraph at lines 20125--20131
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T
1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 20136--20139
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m
/n/10 ylim <-
[1610] [1611] [1612] [1613] [1614]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20437--20437
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 1194) in paragraph at lines 20447--20450
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1615]
Underfull \hbox (badness 1107) in paragraph at lines 20505--20507
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate []
\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to
[1616]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20560--20560
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20567--20567
[]\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)[]
[1617] [1618]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20661--20661
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1619] [1620]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20790--20790
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1621]
Underfull \hbox (badness 7740) in paragraph at lines 20853--20855
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [
]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20901--20901
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1622]
Underfull \hbox (badness 10000) in paragraph at lines 20957--20959
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 polym(*, coefs=<non-NULL>)[]\T1/ptm/m/n/10 , and
[1623]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20994--20994
[] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or
just poly():[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20999--20999
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634]
[1635] [1636]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 21854--21854
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[]
[1637]
Underfull \hbox (badness 6859) in paragraph at lines 21921--21928
[][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21932--21938
[]\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/1
0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 ,
[1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648]
[1649]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22678--22678
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1650] [1651] [1652] [1653] [1654]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22962--22962
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22963--22963
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1655] [1656] [1657] [1658] [1659]
Underfull \hbox (badness 1337) in paragraph at lines 23289--23295
[]\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
[1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667]
Underfull \hbox (badness 10000) in paragraph at lines 23848--23850
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 23848--23850
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 23855--23856
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
[1668] [1669]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 23966--23966
[] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[]
[1670]
Underfull \hbox (badness 1028) in paragraph at lines 24024--24027
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T
1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and
[1671] [1672]
Underfull \hbox (badness 10000) in paragraph at lines 24139--24142
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 7099) in paragraph at lines 24194--24196
[]\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 [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1673]
Underfull \hbox (badness 7099) in paragraph at lines 24258--24260
[]\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 [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1674]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24293--24293
[]\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median,
decreasing=TRUE))[]
[1675]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24369--24369
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1676] [1677]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24486--24486
[]\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with
care)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24487--24487
[]\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long
format[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24488--24488
[]\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time
variable[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24489--24489
[]\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v
ariable[]
[1678] [1679]
Underfull \hbox (badness 10000) in paragraph at lines 24649--24654
[][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[]
[][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r
e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [
][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 24649--24654
[][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing
con-tin-gency ta-bles and con-vert-ing them back to
[1680]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24660--24660
[]\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24661--24661
[]\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24680--24680
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1681]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24784--24784
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
[1682]
Underfull \hbox (badness 1033) in paragraph at lines 24827--24833
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
Underfull \hbox (badness 10000) in paragraph at lines 24848--24851
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r
unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] =
[1683]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24930--24930
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1684]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24959--24959
[]\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
used to fail badly (notably for "Turlach"):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24971--24971
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
[1685] [1686] [1687] [1688] [1689] [1690] [1691]
Underfull \hbox (badness 6268) in paragraph at lines 25429--25434
[][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S
Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo
mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 ,
[1692] [1693] [1694] [1695]
Underfull \hbox (badness 1867) in paragraph at lines 25638--25640
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods.
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 25653--25657
[]\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba
ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25653--25657
\T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where
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 25689--25689
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25696--25696
[]\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[]
[1696] [1697] [1698]
Underfull \hbox (badness 2495) in paragraph at lines 25879--25888
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1699] [1700]
Underfull \hbox (badness 2197) in paragraph at lines 26021--26024
[]\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion,
[]\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and
[1701]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 26041--26041
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
Underfull \hbox (badness 1412) in paragraph at lines 26048--26050
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1702]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26135--26135
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 26160--26160
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 26163--26163
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1703] [1704] [1705]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26392--26392
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 26396--26402
[]\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/
10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in
g only
[1706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26442--26442
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26463--26463
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1707] [1708] [1709]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26655--26655
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1710] [1711] [1712] [1713] [1714] [1715] [1716]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 27035--27035
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1717] [1718]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27216--27216
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 27222--27222
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))
for when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27231--27231
[]\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 27232--27232
[]\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 [1719]
Underfull \hbox (badness 2922) in paragraph at lines 27301--27306
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1720]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27338--27338
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27341--27341
[] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27350--27350
[] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27351--27351
[] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
# (Asym + R0)/2[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27355--27355
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1721]
Underfull \hbox (badness 3240) in paragraph at lines 27409--27412
[][][]\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 graph show-ing the []\T1/pcr/m/n/10 SSasympOff
[1722]
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[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[]
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[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1723]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27516--27516
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[]
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[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
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[] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2),
phi[1]), pos=0, las=1)[]
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[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
[1724]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27593--27593
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
[1725]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27609--27609
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
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[]\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af
ter increasing maxiter !}[]
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[] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[]
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[]\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, control = list(scaleOffset=1))[]
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[] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1
e-11, nDcentral=TRUE), trace=TRUE)[]
[1726] [1727]
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[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1728]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
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[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1729]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1730]
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[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1731]
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[]\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number
of iter...: 0" :[]
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[]\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[]
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[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
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[] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x =
xmid = 2) = 2.5[]
[1732]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
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[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1733]
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[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
Underfull \hbox (badness 6493) in paragraph at lines 28142--28147
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1734]
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[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
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[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
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[]\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[]
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[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
[1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745]
[1746] [1747] [1748]
Underfull \hbox (badness 3396) in paragraph at lines 29062--29064
[]\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
[1749] [1750]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
/pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if
[1751] [1752] [1753]
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[]\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
[1754]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
/pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if
[1755]
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1756]
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[]\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)
[1757] [1758]
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[]\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[]
[1759]
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[]\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
[1760] [1761] [1762]
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[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
[1763]
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[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
Underfull \hbox (badness 1616) in paragraph at lines 30082--30085
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
[1764] [1765]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1766]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1767]
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[]\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was
given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a
[1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776]
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1777] [1778] [1779] [1780] [1781]
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[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
[1782] [1783]
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\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:[]
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[1785] [1786]
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[]\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
[1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794]
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[]\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
[1795] [1796] [1797]
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[]\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno
t compute exact p-value with ties[]
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[]\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9)
# same ties as (4:2, 3:1)[]
[1798] [1799] [1800]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
= getOption("ts.eps"), ...)[]
[1801]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
[1802] [1803]
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[]\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 "")[]
[1804]) (./stats4-pkg.tex
Chapter 11.
[1805] [1806] [1807]
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
Underfull \vbox (badness 10000) has occurred while \output is active [1808]
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[]\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos
er to 0 and 1[]
[1809] [1810] [1811] [1812]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again>
\relax
l.503 ...Package \pkg{stats4}}{show.Rdash.methods}
[1813] [1814] [1815])
(./tcltk-pkg.tex [1816]
Chapter 12.
[1817] [1818] [1819] [1820]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[]
[1821] [1822] [1823]
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[]\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i
ng any Tk or Tcl com-mand by sim-ply run-ning
[1825] [1826] [1827] [1828] [1829] [1830]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1079--1079
[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
[1831] [1832] [1833] [1834] [1835]
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-cep
t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/
n/10 (whose
[1836]) (./tools-pkg.tex
Chapter 13.
[1837]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1838]
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[]\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will
be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1839]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1840]
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[]\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
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n
/10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n
/10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10
,
[1841]
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[]\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE,
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin
e to use. Over-rides any
[1842] [1843]
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
ub-di-rec-tory
[1844] [1845] [1846] [1847] [1848]
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[1849] [1850]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 911--911
[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
[1851] [1852] [1853]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1134--1134
[] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[]
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[]\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[]
[1854]
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[]\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
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a
pre-vi-ous
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\
T1/ptm/m/n/10 and
[1855]
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[]\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in-
her-it-ing from class
[1856] [1857]
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[]\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [
]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1
/ptm/m/n/10 and
[1858] [1859]
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[]\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with
char-ac-ter columns con-tain-ing most
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu
r-rent pack-ages in the CRAN pack-age repos-i-
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\T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta
iner in-for-ma-tion not pro-vided by
[1860]
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[]\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR
AN_current_db []\T1/ptm/m/n/10 and
[1861] [1862]
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[] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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[]\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests",
Underfull \hbox (badness 1558) in paragraph at lines 1714--1722
\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor,
[1863] [1864] [1865]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.GSC}) has been already used, duplicate ignored
<to be read again>
\relax
l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC}
pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
[1866] [1867] [1868]
[1869]
Underfull \hbox (badness 1142) in paragraph at lines 2196--2202
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio
n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the
pack-age
[1870]
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[] \T1/pcr/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option
s: width=100 alt="R logo"}})",[]
Underfull \hbox (badness 2359) in paragraph at lines 2258--2265
[]\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-
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\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-
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\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
[1871]
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\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
[1872]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2384--2384
[]\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str
ong",
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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[]\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests",
Underfull \hbox (badness 1558) in paragraph at lines 2399--2407
\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor,
[1873]
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[]\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[]
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[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
= TRUE)[]
[1874] [1875] [1876] [1877]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2752--2752
[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[]
[1878]
Underfull \hbox (badness 2486) in paragraph at lines 2797--2805
[]\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
[1879] [1880] [1881]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3009--3009
[]\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal =
FALSE)
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[]\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal =
FALSE)[]
[1882] [1883] [1884]
Underfull \hbox (badness 1072) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-
tor of links, as re-turned by
[1885] [1886] [1887] [1888] [1889]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3534--3534
[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
[1890]
Underfull \hbox (badness 5417) in paragraph at lines 3572--3582
[]\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10
, \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10
,
[1891] [1892] [1893]
Underfull \hbox (badness 4108) in paragraph at lines 3782--3789
[]\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
[1894] [1895]
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[]
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[]\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if
in-stalled. This should be run with
[1896] [1897]
Underfull \hbox (badness 7832) in paragraph at lines 4041--4044
[]\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5
.0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti
on
[1898] [1899] [1900] [1901]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4276--4276
[] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[]
[1902] [1903]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 4438--4438
[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts =
"", copyright, bugs)
Underfull \hbox (badness 3118) in paragraph at lines 4449--4453
[]\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m
sgmerge []\T1/ptm/m/n/10 in ad-di-tion to
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig
ht[]\T1/ptm/m/n/10 ' and
[1904]
Underfull \hbox (badness 6859) in paragraph at lines 4469--4474
[]\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/ptm/m/n/10 ' are up-dated from
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[]\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
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\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
[1905] [1906] [1907]
Underfull \hbox (badness 10000) in paragraph at lines 4703--4705
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10
, such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or
[1908]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[]
Underfull \hbox (badness 3240) in paragraph at lines 4746--4749
[]\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 ',
Underfull \hbox (badness 1742) in paragraph at lines 4750--4760
[]\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe
nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4788--4794
[]\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo
r R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4788--4794
\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 ',
[1909]
Underfull \hbox (badness 1571) in paragraph at lines 4816--4820
[]\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
Underfull \hbox (badness 2772) in paragraph at lines 4842--4847
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][
]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat
-ing ex-ist-ing
[1910] [1911]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4984--4984
[]\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[]
[1912]) (./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 `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
[1913] [1914] [1915] [1916]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1917]
Underfull \hbox (badness 10000) in paragraph at lines 378--383
\T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min
imize",
[1918]
Underfull \hbox (badness 10000) in paragraph at lines 384--386
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow
han-dles, by de-fault pro-duced by
[1919]
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[]\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F
irefox window[]
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[]\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
"Firefox"))[]
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[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1920] [1921] [1922]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683
[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
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[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
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[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\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 692--692
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
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[]\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 726--732
[]\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a
spell_package_C_files []\T1/ptm/m/n/10 per-form spell check-
[1923] [1924] [1925] [1926] [1927]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1049--1049
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1928]
Underfull \hbox (badness 1748) in paragraph at lines 1115--1123
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/pcr/m/n/
10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$
\T1/ptm/m/n/10 , in-di-cat-
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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
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\T1/ptm/m/n/10 as [][][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max", 1
) []\T1/ptm/m/n/10 which is []\T1/pcr/m/n/10 1 []\T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1115--1123
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1929]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1930] [1931]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1318--1318
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1932] [1933] [1934] [1935] [1936]
Underfull \hbox (badness 1859) in paragraph at lines 1721--1730
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
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\T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1
/ptm/m/n/10 never re-turns. Do not re-port that
[1937] [1938]
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[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[1939]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1940]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1941]
Underfull \hbox (badness 2277) in paragraph at lines 2076--2081
[]\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p
tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes
[1942]
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[]\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct",
"upper", "xdigit")[]
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[]\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2119--2119
[]\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
Unicode 13.)[]
[1943] [1944] [1945]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2267--2267
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1946]
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1947] [1948]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2489--2489
[] \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")[]
[1949]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[1950]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1951]
Underfull \hbox (badness 1082) in paragraph at lines 2706--2710
[][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab
out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file
s;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2711 ... the Clipboard in MS Windows}{clipboard}
[1952]
Underfull \hbox (badness 1163) in paragraph at lines 2742--2744
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1953]
Underfull \hbox (badness 10000) in paragraph at lines 2835--2837
[]\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
[1954] [1955] [1956] [1957]
Underfull \hbox (badness 10000) in paragraph at lines 3053--3055
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1958] [1959] [1960] [1961]
Underfull \hbox (badness 1762) in paragraph at lines 3346--3349
[]\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 []\T1/pcr/m/n/10 package =
[1962]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3438--3438
[]\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se
ts in the rpart package[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3439--3439
[]\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 '[]
[1963]
Underfull \hbox (badness 2452) in paragraph at lines 3515--3518
[]\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
[1964] [1965] [1966] [1967] [1968] [1969]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3931--3931
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[1970]
Underfull \hbox (badness 4779) in paragraph at lines 4010--4015
[]\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10
was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use
[1971]
Underfull \hbox (badness 1072) in paragraph at lines 4073--4077
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the
[1972]
Underfull \hbox (badness 7238) in paragraph at lines 4129--4134
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1
0 via \T1/ptm/m/n/10 the en-vi-ron-
Underfull \hbox (badness 1337) in paragraph at lines 4129--4134
\T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or
[]\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : /
/ curl . se / libcurl / c /
Underfull \hbox (badness 1184) in paragraph at lines 4144--4160
\T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10
'. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-
[1973]
Underfull \hbox (badness 4660) in paragraph at lines 4261--4264
\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
[1974]
Underfull \hbox (badness 10000) in paragraph at lines 4285--4287
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do
wnload.file[][][] []\T1/ptm/m/n/10 and
[1975] [1976]
Underfull \hbox (badness 1565) in paragraph at lines 4470--4474
[]\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
[1977]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4553--4553
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[1978]
Underfull \hbox (badness 1910) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p
le is run and
Underfull \hbox (badness 1655) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [
]\T1/ptm/m/n/10 sets the same state as
Underfull \hbox (badness 2846) in paragraph at lines 4587--4594
[]\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac
k-age's ex-am-ples. This is cur-
Underfull \hbox (badness 3460) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau
lt", "default",
Underfull \hbox (badness 1931) in paragraph at lines 4594--4601
[]\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di
-cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1979] [1980] [1981] [1982]
Underfull \hbox (badness 5939) in paragraph at lines 4840--4842
[]\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n
/10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault
[1983] [1984]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4983--4983
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1985]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.5054 ...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
<to be read again>
\relax
l.5054 ...mat Unordered and Ordered Lists}{format}
[1986] [1987] [1988]
[1989] [1990] [1991] [1992] [1993]
Underfull \hbox (badness 1622) in paragraph at lines 5577--5581
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
to ex-ter-nal GUIs or to the
[1994] [1995] [1996] [1997] [1998] [1999]
Underfull \hbox (badness 1448) in paragraph at lines 5956--5961
[]\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject
s, cor-re-spond-ing to call-ing
[2000] [2001]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 6106--6106
[]\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 6118--6118
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
[2002] [2003]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6251--6251
[] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 6252--6252
[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
[2004] [2005] [2006]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6462--6462
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[2007]
Underfull \hbox (badness 10000) in paragraph at lines 6546--6548
[]\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
[2008]
Underfull \hbox (badness 1502) in paragraph at lines 6595--6600
[]\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 6595--6600
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[2009] [2010]
Underfull \hbox (badness 10000) in paragraph at lines 6768--6777
[]\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 6768--6777
\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
[2011]
Underfull \hbox (badness 2150) in paragraph at lines 6832--6835
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
[2012]
Underfull \hbox (badness 5175) in paragraph at lines 6848--6851
[]\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc
h database for sub-se-quent use by
[2013]
Underfull \hbox (badness 3118) in paragraph at lines 6971--6973
[]\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
[2014] [2015] [2016]
Underfull \hbox (badness 5091) in paragraph at lines 7146--7148
[]\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 10000) in paragraph at lines 7176--7183
[]\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends
", "Imports", "LinkingTo",
Underfull \hbox (badness 10000) in paragraph at lines 7176--7183
\T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports",
Underfull \hbox (badness 1270) in paragraph at lines 7176--7183
\T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in
-stalls all the pack-ages
Underfull \hbox (badness 1270) in paragraph at lines 7191--7201
\T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla
g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If
[2017]
Underfull \hbox (badness 4441) in paragraph at lines 7234--7237
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed to
Underfull \hbox (badness 2837) in paragraph at lines 7234--7237
[]\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall.
E.g., []\T1/pcr/m/n/10 c("--html",
Underfull \hbox (badness 1424) in paragraph at lines 7242--7245
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
[2018]
Underfull \hbox (badness 2376) in paragraph at lines 7313--7320
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n
/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7313--7320
\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 7313--7320
\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 1087) in paragraph at lines 7321--7324
[]\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt
m/m/n/10 al-ways works pro-vided the pack-age con-tains no
[2019]
Underfull \hbox (badness 1314) in paragraph at lines 7401--7408
[]\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute
all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 7481--7486
[][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac
kages[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7504--7504
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
[2021]
Underfull \hbox (badness 5133) in paragraph at lines 7540--7544
[]\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 7554--7557
[]\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10
DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7601--7601
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[2022] [2023]
Underfull \hbox (badness 4132) in paragraph at lines 7725--7727
[]\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
[2024] [2025] [2026]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7892--7892
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[2027] [2028] [2029]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8035--8035
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
Underfull \hbox (badness 10000) in paragraph at lines 8075--8077
[]\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
[2030] [2031]
Underfull \hbox (badness 10000) in paragraph at lines 8180--8182
[]\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 8185--8187
[]\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 S3 class
[2032] [2033] [2034] [2035]
Underfull \hbox (badness 1859) in paragraph at lines 8413--8416
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
Underfull \hbox (badness 1052) in paragraph at lines 8432--8442
\T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/
n/10 el-e-ments with names start-ing with a suit-able pre-fix
[2036]
Underfull \hbox (badness 1655) in paragraph at lines 8507--8510
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d
b"[]\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 8518--8518
[]\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8526--8526
[]\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 8534--8534
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[2037] [2038]
Underfull \hbox (badness 1917) in paragraph at lines 8621--8623
[]\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/
n/10 ,
[2039] [2040] [2041] [2042]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8893--8893
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8894--8894
[] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8895--8895
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[2043]
Underfull \hbox (badness 10000) in paragraph at lines 8923--8925
[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\
T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 8937--8939
[]\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut
, al-low-ing things like []\T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8945--8950
[]\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,
[2044]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8991--8991
[] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8992--8992
[] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[]
[2045] [2046]
Underfull \hbox (badness 10000) in paragraph at lines 9121--9126
[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade",
Underfull \hbox (badness 10000) in paragraph at lines 9128--9131
[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("installed", "not
[2047]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9245--9245
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[2048] [2049] [2050]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9418--9418
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[2051]
Underfull \hbox (badness 1789) in paragraph at lines 9551--9553
[]\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
[2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060]
Underfull \hbox (badness 5203) in paragraph at lines 10124--10127
[]\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
[2061] [2062] [2063]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10374--10374
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[2064] [2065]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10535--10535
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[2066] [2067] [2068]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10716--10716
[]\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[]
[2069]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10802--10802
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10805--10805
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10810--10810
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2070]
Underfull \hbox (badness 2027) in paragraph at lines 10882--10885
[]\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force
s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL
[2071] [2072] [2073] [2074]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11161--11161
[]\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC",
"HPD"),
Overfull \hbox (6.78088pt too wide) in paragraph at lines 11162--11162
[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
Underfull \hbox (badness 10000) in paragraph at lines 11169--11174
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 11169--11174
\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 11169--11174
[]\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER
S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2075] [2076] [2077] [2078]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11402--11402
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2079] [2080] [2081] [2082]
Underfull \hbox (badness 10000) in paragraph at lines 11663--11667
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[]
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[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
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[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
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[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
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[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
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[]\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n
ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me
nt vari-
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\T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10
. If this is set, then it takes prece-dence over
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[]\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 '[]
[2089]
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[] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news",
"Rfunctions",[]
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[] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig
nettes"),[]
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[] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s
ubject",[]
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[] \T1/pcr/m/n/10 "subject:descending", "size", "size:de
scending"),[]
[2090]
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\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,
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\T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re
-verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or
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[]\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes","
Rfunctions"))[]
[2091]
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[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/
m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style
[2092]
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[][][]$\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 /
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[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[2093] [2094] [2095]
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[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i
s now taken from the en-vi-ron-ment vari-able
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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][]
[]\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m
/n/10 out-put in
[2096] [2097]
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[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[2098]
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[]\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
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[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows
and
[2099]
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[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
con-fig-ured the map-ping of font num-bers to fonts, and
[2100] [2101] [2102] [2103]
Underfull \hbox (badness 1888) in paragraph at lines 13188--13191
[]\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-der. Where
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2104]
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[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
[2105]
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[]\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
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[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
[2106] [2107] [2108]
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2109]
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[]\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir
ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2110] [2111] [2112]
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[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
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[]\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
[][][]\T1/pcr/m/n/10 deparse[][][](control = <S>) []\T1/ptm/m/n/10 will not ha
ve
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha
s only a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic
h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it
y rea-sons;
[2113]
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[]\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau
lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to
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[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2114]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
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[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
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[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[2115] [2116] [2117]
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[]\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
[2118]
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[]\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se
e
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[][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/
m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu-
[2119]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau
lt) then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt
m/m/n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 14252--14259
\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$"[]\T1/ptm/m/n/10 ) and
[2120] [2121]
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\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/
n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on
some plat-forms),
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\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --
exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n
/10 ' (and sim-i-lar) and on Win-dows
[2122]
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[]\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p
cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able
[2123]
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[]\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t
o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment
vari-able
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
[2124] [2125] [2126]
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[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
[2127] [2128] [2129] [2130] [2131] [2132]
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
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[]\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
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\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
[2133]
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins
talled.packages[][][](lib.loc =
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[]\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be
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\T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15243--15248
[]\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac
he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
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[]\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n
/10 available.packages(contriburl =
Underfull \hbox (badness 1226) in paragraph at lines 15279--15284
\T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa
ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
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[]\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
[2134]
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[][][]\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.pa
ckages[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt")
[2135] [2136] [2137]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v
i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,
[2138]
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[]\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:[]
[2139]
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[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
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[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
[2140] [2141]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2142]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil
l delete a menu and all of its items and sub-menus.
[2143] [2144]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2145]
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[]\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : []
\T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n
/10 and
Underfull \hbox (badness 10000) in paragraph at lines 16069--16071
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. []\T1/pcr/m/n/10 file =
[2146] [2147] [2148]) [2149] [2150] (./KernSmooth-pkg.tex
Chapter 15.
[2151]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2152] [2153] [2154] [2155] [2156]
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[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2157] [2158] [2159] [2160]) (./MASS-pkg.tex
Chapter 16.
[2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182]
[2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193]
[2194]
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[2195] [2196] [2197] [2198]
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[]\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
[2199] [2200] [2201]
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[]\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo
gnormal"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi
al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
/10 "Poisson"[]\T1/ptm/m/n/10 ,
[2202] [2203]
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[]\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
[2204] [2205] [2206]
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[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
[2207]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
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[2219]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv
et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and
[2220] [2221] [2222] [2223] [2224] [2225] [2226]
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[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[2227] [2228] [2229]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[2241] [2242] [2243]
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2244]
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[]\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")
[2245] [2246]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6151 ...sical N, P, K Factorial Experiment}{npk}
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\relax
l.6151 ...sical N, P, K Factorial Experiment}{npk}
[2247] [2248] [2249]
[2250] [2251] [2252]
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[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2253]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2254] [2255] [2256] [2257] [2258] [2259]
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[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
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[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
[2260]
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[]\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 ) =
[2261]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2262] [2263]
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[]\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than
[]\T1/pcr/m/n/10 min(p,
[2264] [2265]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2266]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2267] [2268] [2269] [2270] [2271] [2272]
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[]\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
[2273] [2274]
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[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\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
[2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285]
[2286] [2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294]
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[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2295]
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[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\
T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n
/10 ,
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[]\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-l
arly),
[2296]
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[]\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25)
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[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
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[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2297] [2298] [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] [2307]
[2308] [2309]) (./Matrix-pkg.tex [2310]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 35--38
[]\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
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2311]
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[]\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
[2312]
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[]\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 153--156
\T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor
, these ar-gu-ments will be con-cate-nated to a new
[2313]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\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
[2314] [2315]
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[] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym
metry property[]
[2316]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
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[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
[2317]
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[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2318]
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[]\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:[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>) 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 '[]
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[]\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}"}.[]
[2319]
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[] \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?[]
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[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
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[]\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[]
[2320]
Underfull \hbox (badness 1874) in paragraph at lines 737--740
[]\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 https : / / netlib . org /
[2321] [2322]
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\T1/ptm/m/n/10 sity'' of []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/
10 y[]\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n/10 code in []
\T1/pcr/m/n/10 selectMethod(cbind2,
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[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/
10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met
h-ods:
[2323]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2324]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "pMatrix") []\T1/ptm/m/n/10
re-turns the per-mu-ta-tion
[2325]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1154 ...- 'Matrix' S4 Generic and Methods}{chol}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
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<to be read again>
\relax
l.1154 ...- 'Matrix' S4 Generic and Methods}{chol}
[2326] [2327]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2328]
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[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
[2329]
Underfull \hbox (badness 2277) in paragraph at lines 1424--1427
[]\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
[2330]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\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(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
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[]\T1/pcr/m/n/9 str(re <- lapply(rr, expand), max.level=2) ## each has a \TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 matrix[]
[2331]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("Cholesky", ...) []\T1/ptm/m/n/10 or
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[]\T1/pcr/m/n/10 new("BunchKaufman", ...)[]\T1/ptm/m/n/10 , etc, or rather by c
alls of the form [][][]\T1/pcr/m/n/10 chol[][][](pm) []\T1/ptm/m/n/10 or
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[]\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
[2332]
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\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 .
Hence, for com-pat-i-bil-ity, the []\T1/pcr/m/n/10 "Cholesky" []\T1/ptm/m/n/10
and
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
has been already used, duplicate ignored
<to be read again>
\relax
l.1657 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again>
\relax
l.1657 ... Row and Column Sums and Means}{colSums}
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icate ignored
<to be read again>
\relax
l.1658 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1681 \aliasA{rowMeans}{colSums}{rowMeans}
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ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
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\relax
l.1694 \aliasA{rowSums}{colSums}{rowSums}
[2333pdfTeX warning (ext4): destinati
on with the same identifier (name{Rfn.rowMeans,diagonalMatrix.Rdash.method}) ha
s been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.1733 ## S4 method for signature 'CsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.rowSums,diagonalMatrix.Rdash.method}) h
as been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.1733 ## S4 method for signature 'CsparseMatrix'
]
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[]\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
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\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 fr
om a
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[][][]\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/1
0 , since
[2334] [2335]
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[]\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
[2336] [2337] [2338] [2339] [2340] [2341]
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[]\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
[2342] [2343] [2344]
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[]\T1/pcr/m/n/10 signature(from = "dgTMatrix", to = "matrix")[]\T1/ptm/m/n/10 ,
and typ-i-cally co-er-cion
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[]\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and []
[][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr
/m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other
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[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
more than one pos-si-ble
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[]\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 a
nd [][][]\T1/pcr/m/n/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 ;
[2345]
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[] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE,
kind)[]
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[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
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[]\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 2793--2798
[][][]\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
[2346]
Underfull \hbox (badness 1097) in paragraph at lines 2816--2819
[]\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 ldiMat
rix[][][] []\T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2829--2834
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][] []\T1/ptm/m/n/10 (the re-sult-ing clas
s de-pend-ing on []\T1/pcr/m/n/10 shape []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 k
ind[]\T1/ptm/m/n/10 ) rep-re-sen-ta-tion of
[2347]
Underfull \hbox (badness 3646) in paragraph at lines 2925--2928
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a []
[][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma
trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 6542) in paragraph at lines 2960--2964
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr
oup meth-ods re-turn a
Underfull \hbox (badness 4518) in paragraph at lines 2969--2975
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10
: the re-sult is from class
[2348pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coer
ce,diagonalMatrix,nMatrix.Rdash.method}) has been already used, duplicate ignor
ed
<argument> ...shipout:D \box_use:N \l_shipout_box
l.2975
]
Underfull \hbox (badness 10000) in paragraph at lines 2976--2980
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j
ect of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 2986--2990
[][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes
e 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
[2349] [2350]
Underfull \hbox (badness 10000) in paragraph at lines 3166--3168
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 :
this group con-tains
[2351] [2352]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 3312--3312
[]\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe
rent from the random one[]
[2353]
Underfull \hbox (badness 2469) in paragraph at lines 3422--3425
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][]
[]\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/
ptm/m/n/10 , via
Underfull \hbox (badness 10000) in paragraph at lines 3445--3450
[]\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as
Underfull \hbox (badness 2020) in paragraph at lines 3445--3450
[][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10
for ef-fi-ciency rea-sons only check the di-
Underfull \hbox (badness 1748) in paragraph at lines 3451--3460
\T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p
tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion
Underfull \hbox (badness 1590) in paragraph at lines 3451--3460
\T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][
][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see
[]\T1/pcr/m/n/10 selectMethod("coerce",
[2354] [2355]
Underfull \hbox (badness 10000) in paragraph at lines 3599--3603
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsCMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 2103) in paragraph at lines 3599--3603
[]\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v
ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 ,
[2356]
Underfull \hbox (badness 1571) in paragraph at lines 3649--3652
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10
: Re-turns (and stores) the
[2357] [2358]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3818
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class []
\T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse
Matrix"[]\T1/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3813--3818
\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 "compMatri
x" []\T1/ptm/m/n/10 by class
Underfull \hbox (badness 1400) in paragraph at lines 3825--3828
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10
: if []\T1/pcr/m/n/10 uplo ==
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 3896--3898
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsyMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1365) in paragraph at lines 3938--3941
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10
, or []\T1/pcr/m/n/10 x = "dsyMatrix"
[2360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3983--3983
[]\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ
internally :[]
[2361]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4116--4116
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
[2362]
Underfull \hbox (badness 3635) in paragraph at lines 4179--4183
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla
ss
Underfull \hbox (badness 10000) in paragraph at lines 4188--4191
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
[2363]
Underfull \hbox (badness 10000) in paragraph at lines 4193--4197
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n
/10 : the
[2364] [2365pdfTeX warning (ext4): destination with the same identifier (name{R
fn.coerce,dtrMatrix,dgeMatrix.Rdash.method}) has been already used, duplicate i
gnored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.4347 \item[\code{diag}:]
Object of class \code{"character"}. Must be]
Underfull \hbox (badness 2065) in paragraph at lines 4378--4382
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix", b = "....")[]\T1/ptm/m/n/10 efficie
ntely use a ``for-ward-solve'' or
[2366] [2367] [2368] [2369]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 4635--4635
[]\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe
ll-Boeing/counterx/counterx.html[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 4642--4642
[] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB
/Boeing/msc00726.tar.gz"))))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4646--4646
[]\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary
dir./folder:[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4649--4649
[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4659--4659
[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2370] [2371] [2372] [2373]
Underfull \hbox (badness 10000) in paragraph at lines 4937--4942
[]\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10
, and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][
][][]\T1/ptm/m/n/10 ,
[2374]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5018--5018
[]\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 5020--5020
[] \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 5024--5024
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2375]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5031--5031
[] \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 '[]
[2376] [2377]
Underfull \hbox (badness 4120) in paragraph at lines 5170--5173
[]\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
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5188--5188
[]\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) #
failed for 2 days ..[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5208--5208
[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5214--5214
[] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,
border.col=NA)[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5215--5215
[] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[]
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5219--5219
[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
[2378]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227
[]\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 5230--5230
[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2379]
Underfull \hbox (badness 1817) in paragraph at lines 5326--5335
[]\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 wit
hin the
Underfull \hbox (badness 10000) in paragraph at lines 5368--5370
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
Underfull \hbox (badness 7081) in paragraph at lines 5370--5373
[]\T1/pcr/m/n/10 signature(from = "integer", to = "indMatrix")[]\T1/ptm/m/n/10
: This en-ables typ-i-cal
Underfull \hbox (badness 4556) in paragraph at lines 5376--5383
[]\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : T
he list must have two
[2380]
Underfull \hbox (badness 3302) in paragraph at lines 5401--5404
[]\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 :
re-turn the kro-necker
[2381] [2382] [2383] [2384]
Overfull \hbox (138.78088pt too wide) in paragraph at lines 5776--5776
[]\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, tol1 = 8
* tol, checkDN = TRUE, ...)[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5782--5782
[]\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, checkDN
= TRUE, ...)[]
[2385]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5841--5841
[]\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if
not "formally"[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5845--5845
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g
eneric from base[]
[2386]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5937--5937
[]\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even
if not "formally"[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5962--5962
[]\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames
= FALSE)
[2387] [2388]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042
[]\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 6043--6043
[] \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 6050--6050
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2389] [2390]
Underfull \hbox (badness 1062) in paragraph at lines 6204--6207
[]\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 6233--6236
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2391]
Underfull \hbox (badness 2635) in paragraph at lines 6402--6407
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ldenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6402--6407
\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 "Matri
x"[]\T1/ptm/m/n/10 , by class
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 6410--6413
[]\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.,
Underfull \hbox (badness 10000) in paragraph at lines 6566--6576
[]\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T
1/ptm/m/n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6566--6576
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc
r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10
, and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\
T1/ptm/m/n/10 --in
[2393]
Underfull \hbox (badness 3179) in paragraph at lines 6648--6651
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2394]
Underfull \hbox (badness 10000) in paragraph at lines 6751--6754
[]\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.,
[2395]
Underfull \hbox (badness 10000) in paragraph at lines 6830--6833
[]\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.,
[2396]
Underfull \hbox (badness 1430) in paragraph at lines 6904--6910
\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, []\T1/pcr/
m/n/10 lu(x,
[2397]
Underfull \hbox (badness 1675) in paragraph at lines 6929--6932
[]\T1/pcr/m/n/10 lu() []\T1/ptm/m/n/10 is a generic func-tion with spe-cial met
h-ods for dif-fer-ent types of ma-tri-ces. Use
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7001--7001
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2398] [2399]
Underfull \hbox (badness 10000) in paragraph at lines 7141--7144
[]\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm
/m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x
,
[2400]
Underfull \hbox (badness 1490) in paragraph at lines 7163--7165
[]\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/
m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][
] []\T1/ptm/m/n/10 and (one case of)
[2401] [2402]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again>
\relax
l.7358 \aliasA{det}{Matrix-class}{det}
[2403pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.coerce,Matrix,denseMatrix.Rdash.method}) has
been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.7439 \item[dim]
\code{signature(x = "Matrix")}: extract matrix dimensions]
Underfull \hbox (badness 1337) in paragraph at lines 7446--7449
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set
the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a
Underfull \hbox (badness 10000) in paragraph at lines 7459--7462
Underfull \hbox (badness 10000) in paragraph at lines 7469--7471
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This
re-lies on a cor-rect
[2404]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.7532 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again>
\relax
l.7629 ...A{crossprod}{matrix-products}{crossprod}
pdfTeX warning (ext4): destin
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l.7723 ...tcrossprod}{matrix-products}{tcrossprod}
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\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/
pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
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[]\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr
ix mul-ti-pli-ca-tion. Mul-ti-
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\T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas
s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-
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[]\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2409]
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[]\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 []\T1/pcr/m/n/10 X <-
[2410] [2411]
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[] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
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[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ndenseMatrix"[]\T1/ptm/m/n/10 .
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\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 "Matri
x"[]\T1/ptm/m/n/10 , by class
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[]\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.,
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[]\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N
ote that these co-er-cions
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[]\T1/ptm/m/n/10 fast sim-
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l.8626 \HeaderA{norm}{Matrix Norms}{norm}
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[2416]
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[]\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n
/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri
x[]\T1/ptm/m/n/10 ,
[2417]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2418]
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[]\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.,
[2419]
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[]\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.,
[2420] [2421]
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op =
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=
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=
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p =
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op =
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=
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=
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op =
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=
[2422]
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=
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p =
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op =
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=
[2423]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") []\T1/ptm/m/n/10 and ot
her sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "integer", to = "pMatrix")[]\T1/ptm/m/n/10 :
This is en-ables typ-i-cal
[2424]
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "matrix")[]\T1/ptm/m/n/10 : c
o-er-cion to a tra-di-tional
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[]\T1/pcr/m/n/10 signature(x = "pMatrix", logarithm="logical")[]\T1/ptm/m/n/10
: Since per-mu-ta-
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\T1/ptm/m/n/10 trix; note that []\T1/pcr/m/n/10 solve(P) []\T1/ptm/m/n/10 is id
en-ti-cal to []\T1/pcr/m/n/10 t(P) []\T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-c
es. See
[2425]
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[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of []
\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2426] [2427]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.9569 \aliasA{qr}{qr-methods}{qr}
[2428]
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[]\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![]
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[]\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[]
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[]\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[]
[2429]
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[]\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10
qr[][][](x, tol,
[2430]
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 , it cor-re-sponds to
[2431]
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[]\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"[]
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[]\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol
= 1e-7)) # all 14[]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war
ning+ ~1.5 sec (2013)[]
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[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
[2432]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco
nd}) has been already used, duplicate ignored
<to be read again>
\relax
l.9893 ... the Reciprocal Condition Number}{rcond}
[2433]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2434] [2435] [2436]
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\T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr
ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n
/10 is not
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class []\T1/pcr/m/n
/10 "Matrix"[]\T1/ptm/m/n/10 ) or tra-di-tional
[2439]
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[] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[]
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[]\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[]
[2440]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
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l.10470 \aliasA{solve}{solve-methods}{solve}
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[]\T1/pcr/m/n/10 ## solve(a, b, ...) # the two-argument version, almost always
preferred to
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[]\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "
D", "P", "Pt"), ...)[]
[2441]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 solve []\T1/ptm/m/n/10 meth-ods for a
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[]\T1/ptm/m/n/10 (for all []\T1/pcr/m/n/10 b[]\T1/ptm/m/n/10 ) work via []\T1/p
cr/m/n/10 as(a,
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 (
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 (
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\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-met-ric,
[2442]
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
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[]\T1/ptm/m/n/10 works via []\T1/pcr/m/n/10 as(b,
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via []\T1/pcr/m/n/10 as(a,
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[][][]\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
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 sparseLU[][][][]\T1/ptm/m/n/10 ,
and
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[]\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2443]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs
parse)[]
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs
parse,[]
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[]\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,
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[]\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)
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[]\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c
on-trasts to be ap-plied to the
[2444]
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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[]\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 1668) in paragraph at lines 10838--10843
[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2445]
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[] \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 10919--10919
[] \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 10920--10920
[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2446] [2447]
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[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
[2448]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2449]
Underfull \hbox (badness 10000) in paragraph at lines 11234--11237
[]\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
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[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
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[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2450]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\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)[]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[]
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[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
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Underfull \hbox (badness 6842) in paragraph at lines 11411--11414
[]\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\
T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods
[2452]
Underfull \hbox (badness 10000) in paragraph at lines 11446--11450
[][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences,
such 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
<to be read again>
\relax
l.11486 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2453] [2454]
Underfull \hbox (badness 10000) in paragraph at lines 11616--11618
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")[]\T1/ptm/m/n/10 : For []\
T1/pcr/m/n/10 solve(a,b)[]\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 11644--11644
[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
[2455]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
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[]\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-
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\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 "
lsparseVector"[]\T1/ptm/m/n/10 ,
[2456]
Underfull \hbox (badness 10000) in paragraph at lines 11834--11837
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/
n/10 co-erces sparse
[2457]
Underfull \hbox (badness 10000) in paragraph at lines 11874--11879
[]\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 11889--11891
[][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str
uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*,
[2458] [2459]
Underfull \hbox (badness 2310) in paragraph at lines 12014--12020
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more
usual con-struc-tor of such ma-tri-ces. Then,
[2460]
Underfull \hbox (badness 6188) in paragraph at lines 12105--12107
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix", to = "symmetricMatrix")[]\T1/ptm
/m/n/10 : and many
[2461]
Underfull \hbox (badness 2591) in paragraph at lines 12131--12136
\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-m
eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
Underfull \hbox (badness 2057) in paragraph at lines 12207--12209
[]\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.,
[2462] [2463]
Underfull \hbox (badness 6641) in paragraph at lines 12294--12297
[]\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 ) h
ave meth-ods with
Underfull \hbox (badness 5133) in paragraph at lines 12338--12342
[]\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 12338--12342
\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
[2464] [2465]
Underfull \hbox (badness 7649) in paragraph at lines 12445--12447
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2466] [2467]
Underfull \hbox (badness 10000) in paragraph at lines 12563--12565
[]\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 ,
though
[2468]
Underfull \hbox (badness 1668) in paragraph at lines 12692--12695
[][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac
k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac
kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes
[2469]
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[]\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
[2470]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\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)[]
[2471] [2472]
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[] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/
x))$modulus))[]
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[] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/
x))$modulus))[]
[2473]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2474]
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref) removing `\Rpercent' on input line 13194.
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref) removing `\Rpercent' on input line 13194.
[2475]
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[]\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero
s" to drop0()[]
[2476]) (./boot-pkg.tex
Chapter 18.
[2477] [2478] [2479] [2480] [2481] [2482] [2483]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532
[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2484]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\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 585--590
[]\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-
[2485] [2486] [2487]
Underfull \hbox (badness 1881) in paragraph at lines 826--828
[]\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 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo
ot.ci[][][][]\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 j
ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T
1/ptm/m/n/10 ,
[2488]
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[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
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[2490] [2491]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\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 1084--1093
\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 1105--1111
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2492] [2493] [2494] [2495]
Underfull \hbox (badness 1571) in paragraph at lines 1445--1447
[]\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-
[2496] [2497] [2498] [2499] [2500]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2501] [2502] [2503]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2505]
Underfull \hbox (badness 6268) in paragraph at lines 2084--2086
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2506] [2507] [2508]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\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
[2509]
Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat
istic []\T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2432--2434
[]\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 2440--2441
[][][]\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 ,
[2510] [2511]
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[]\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/1
0 is the sam-ple
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\T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr
/m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T
1/ptm/m/n/10 is used. This is mul-ti-plied by
[2512] [2513] [2514] [2515] [2516]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
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[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2517] [2518] [2519]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr
ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/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 ,
[2520]
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[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2521] [2522] [2523]
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[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2524] [2525] [2526] [2527] [2528] [2529] [2530]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2531] [2532]
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[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2533] [2534] [2535] [2536]
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[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2537] [2538]
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[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the
r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a
re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to
[2539] [2540] [2541] [2542] [2543] [2544] [2545] [2546] [2547]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2548] [2549] [2550] [2551]
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[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
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\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2552]
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[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2561]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
[]\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less
than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then
[2562]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s
addle.distn"[]\T1/ptm/m/n/10 . See the help file for
[2563] [2564] [2565] [2566]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
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[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2569] [2570] [2571]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\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
[2572] [2573]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2574] [2575] [2576] [2577] [2578] [2579] [2580] [2581]) (./class-pkg.tex
[2582]
Chapter 19.
[2583] [2584] [2585] [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593]
[2594] [2595] [2596] [2597] [2598]) (./cluster-pkg.tex
Chapter 20.
[2599] [2600] [2601]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253
[] \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 254--254
[] \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 255--255
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2602] [2603]
Underfull \vbox (badness 10000) has occurred while \output is active [2604]
[2605]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
[] \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 523--523
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2606] [2607]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638
[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
[2608]
Underfull \hbox (badness 3078) in paragraph at lines 691--694
[]\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
[2609] [2610]
Underfull \hbox (badness 2941) in paragraph at lines 791--794
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\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 ,
[2611]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
Underfull \hbox (badness 10000) in paragraph at lines 881--883
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2612]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2613]
Underfull \hbox (badness 4872) in paragraph at lines 992--994
[]\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 1006--1010
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2614] [2615]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1121--1121
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1138--1138
[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
Underfull \vbox (badness 10000) has occurred while \output is active [2616]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1176--1176
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
Underfull \hbox (badness 4144) in paragraph at lines 1208--1212
[]\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
[2617]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1284--1284
[] \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 1290--1290
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2618] [2619] [2620]
Underfull \hbox (badness 10000) in paragraph at lines 1477--1480
Underfull \hbox (badness 10000) in paragraph at lines 1494--1498
[][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds
cale[][][][]\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/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1518--1518
[]\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 1528--1528
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2621]
Underfull \hbox (badness 5741) in paragraph at lines 1568--1571
[]\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d
er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2622]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1637--1637
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2623]
Underfull \hbox (badness 1552) in paragraph at lines 1686--1688
[]\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n
/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se
e
Underfull \hbox (badness 1629) in paragraph at lines 1699--1703
[]\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault
\T1/ptm/m/n/10 for all nu-meric
Underfull \hbox (badness 3746) in paragraph at lines 1699--1703
\T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T
1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r
e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see
[2624]
Underfull \hbox (badness 1540) in paragraph at lines 1775--1783
\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 $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 =
[2625]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1867--1867
[]\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1886--1886
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2626] [2627] [2628] [2629] [2630]
Underfull \hbox (badness 10000) in paragraph at lines 2207--2210
Underfull \hbox (badness 3179) in paragraph at lines 2221--2227
[][][]\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/1
0 ellipsoid []\T1/ptm/m/n/10 ob-jects.
[2631] [2632]
Underfull \hbox (badness 10000) in paragraph at lines 2379--2382
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2633]
Underfull \hbox (badness 1292) in paragraph at lines 2447--2450
[]\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10
, the num-ber of it-er-a-tions needed and
[2634]
Underfull \hbox (badness 6675) in paragraph at lines 2456--2458
[]\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 2479--2482
[][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f
anny[][][][]\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 ,
[2635] [2636]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 2608--2608
[]\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES
= FALSE, ...)
[2637]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 2655--2655
[] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k
<= k, table(cl.k) >= 2)[]
[2638]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2760--2760
[]\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 ):[]
[2639]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2839--2839
[] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[]
[2640] [2641] [2642]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2643] [2644]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3171--3171
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2645] [2646] [2647]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3367--3367
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3368--3368
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2648]
Underfull \hbox (badness 10000) in paragraph at lines 3435--3438
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m
/n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <-
[2649]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3485--3485
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3486--3486
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2650] [2651] [2652]
Underfull \hbox (badness 10000) in paragraph at lines 3671--3674
[]\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 [][][]\T1/pcr/m/n/10 pam[]
[][](*,
Underfull \hbox (badness 1448) in paragraph at lines 3671--3674
\T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p
tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is
[2653]
Underfull \hbox (badness 10000) in paragraph at lines 3734--3739
[][][]\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.de
fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 ,
[2654]
Underfull \hbox (badness 1748) in paragraph at lines 3796--3801
\T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p
tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx
<-
Underfull \hbox (badness 6268) in paragraph at lines 3808--3811
[][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o
bject[][][][]\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/1
0 hclust[][][][]\T1/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 ,
[2655] [2656] [2657]
Underfull \hbox (badness 10000) in paragraph at lines 3993--3996
[][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag
nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4024--4027
[][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl
ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2658]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4077--4077
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
[2659]
Underfull \hbox (badness 2035) in paragraph at lines 4088--4090
[]\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
[2660] [2661] [2662]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4281--4281
[] \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 4283--4283
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2663] [2664]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4426--4426
[]\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 4435--4435
[] \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 4437--4437
[] \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 4440--4440
[]\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 4442--4442
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4449--4449
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2665] [2666] [2667] [2668] [2669] [2670] [2671]
Underfull \hbox (badness 10000) in paragraph at lines 4823--4829
[]\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i
s slightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4839--4841
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4852--4852
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4854--4854
[]\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s medoid indices == pam(xclara, 3)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4864--4864
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2672]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4868--4868
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2673]) (./codetools-pkg.tex [2674]
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
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[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2675]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage
Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2676]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2677] [2678] [2679]) (./foreign-pkg.tex [2680]
Chapter 22.
Underfull \hbox (badness 10000) in paragraph at lines 33--37
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p
cr/m/n/10 https : / / support .
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\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
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\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2681]
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
[2682] [2683]
Underfull \hbox (badness 3601) in paragraph at lines 237--245
[]\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 ,
[2684]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2685] [2686] [2687]
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[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2688]
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[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-ent lev-
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\T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul
t), the first orig-i-nal value la-bel is
Underfull \hbox (badness 2269) in paragraph at lines 505--514
\T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p
cr/m/n/10 paste0(label,
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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
du-
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\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup
licated_"[]\T1/ptm/m/n/10 ) if
[2689]
Underfull \hbox (badness 10000) in paragraph at lines 550--558
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com /
en-[]us / windows / win32 / intl /
Underfull \hbox (badness 7613) in paragraph at lines 568--574
[]\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute
[2690]
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[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
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[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2691]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657
[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
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[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
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[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2692] [2693]
Underfull \hbox (badness 10000) in paragraph at lines 812--813
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[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2694]
Underfull \hbox (badness 10000) in paragraph at lines 869--873
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
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\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 869--873
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
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\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2695]
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[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2696]
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[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2697] [2698]
Underfull \hbox (badness 10000) in paragraph at lines 1076--1077
[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase
/ format / data _ types .
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[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2699] [2700]
Underfull \hbox (badness 10000) in paragraph at lines 1270--1276
[]\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig
n:::writeForeignStata[]\T1/ptm/m/n/10 ,
[2701]
Underfull \hbox (badness 2088) in paragraph at lines 1296--1299
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid
e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET
[2702]) (./lattice-pkg.tex
Chapter 23.
[2703]
Underfull \hbox (badness 2073) in paragraph at lines 117--121
\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
Underfull \hbox (badness 10000) in paragraph at lines 117--121
\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm /
ms / departments / sia /
[2704] [2705]
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"),[]
[2706]
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"),[]
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[] \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"),[]
[2707] [2708] [2709] [2710]
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
[2711] [2712] [2713] [2714]
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
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2715]
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 sho
uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2716] [2717]
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
[2718] [2719] [2720]
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 ,
[2721]
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/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 ,
[2722]
Underfull \vbox (badness 10000) has occurred while \output is active [2723]
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
[2724]
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
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T
1/ptm/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
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
[2725] [2726] [2727] [2728]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
[2729]
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-fie
d, the 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 firs
t checked. If
[2730] [2731] [2732]
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"),[]
[2733] [2734] [2735] [2736] [2737]
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"),[]
[2738] [2739]
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/
pcr/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/ptm/m/n/10 must have the same lengths as
[2740]
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[]\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 2919--2923
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra
ster[][][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2925--2927
[]\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][]
[]\T1/ptm/m/n/10 when
Underfull \hbox (badness 1609) in paragraph at lines 2977--2983
[]\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 2977--2983
\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 2977--2983
\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
[2741]
Underfull \hbox (badness 2486) in paragraph at lines 3001--3005
[]\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
[2742]
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[] \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 3105--3105
[] \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 3106--3106
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
[2743]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3129--3129
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2744]
Underfull \hbox (badness 2913) in paragraph at lines 3187--3194
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3187--3194
[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
[2745] [2746] [2747]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3475 \aliasA{parallel}{B\_08\_splom}{parallel}
[2748]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3517--3517
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2749] [2750] [2751] [2752] [2753]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3876--3876
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2754] [2755]
Underfull \hbox (badness 2277) in paragraph at lines 3970--3974
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault
set-tings by
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2756]
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[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
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[]\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
[2757]
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[]\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 4153--4157
[]\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren
t set-tings (ob-tained by
[2758]
Underfull \hbox (badness 5161) in paragraph at lines 4218--4222
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell
is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4218--4222
\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
[2759] [2760]
Underfull \hbox (badness 1067) in paragraph at lines 4336--4346
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/
10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 ,
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[]\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 4336--4346
[]\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super
pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points
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[]\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used
only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/
n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10
for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl
ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10
plot.polygon []\T1/ptm/m/n/10 and
[2761] [2762] [2763] [2764] [2765]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4768--4768
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2766] [2767]
Underfull \vbox (badness 1092) has occurred while \output is active [2768]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4958
[]\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 .
[2769] [2770]
Underfull \hbox (badness 1442) in paragraph at lines 5087--5090
[]\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle
s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and
[2771] [2772] [2773] [2774] [2775]
Underfull \hbox (badness 3646) in paragraph at lines 5426--5429
[][][]\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-call
y the en-try for
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[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
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[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2776]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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[]\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the
left of pan-els us-ing
[2777]
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[]\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect,
which is to draw a strip ap-pro-pri-ate for
[2778] [2779]
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[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
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[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
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[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
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[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
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[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
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[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
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[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
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[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
[2780]
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[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2781]
Underfull \hbox (badness 2538) in paragraph at lines 5907--5911
\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul
t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e
x-tra pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5918--5925
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the
se are used (in com-bi-na-tion with
[2782] [2783]
Underfull \hbox (badness 10000) in paragraph at lines 6071--6075
[][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt
ice[][][][]\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 ,
[2784]
Underfull \vbox (badness 10000) has occurred while \output is active [2785]
[2786]
Underfull \hbox (badness 4242) in paragraph at lines 6218--6223
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2787] [2788]
Underfull \hbox (badness 3601) in paragraph at lines 6334--6339
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m
/n/10 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 6334--6339
\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa
ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2789]
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[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2790] [2791]
Underfull \hbox (badness 1888) in paragraph at lines 6553--6560
[]\T1/pcr/m/n/10 at []\T1/ptm/m/n/10 can be a nu-meric vec-tor, []\T1/pcr/m/n/1
0 col.regions []\T1/ptm/m/n/10 a vec-tor of col-ors, and
[2792]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
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[]\T1/pcr/m/n/10 shade.colors.palette []\T1/ptm/m/n/10 func-tion should re-turn
a valid color. The
[2793] [2794] [2795] [2796] [2797]
Underfull \hbox (badness 1320) in paragraph at lines 7016--7023
[]\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p
anel func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 7016--7023
\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
[2798] [2799]
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[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
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[]\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi
s func-tion is passed
[2800] [2801]
Underfull \hbox (badness 10000) in paragraph at lines 7221--7224
\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
[2802] [2803]
Underfull \hbox (badness 2012) in paragraph at lines 7387--7390
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2804]
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[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2805] [2806]
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[]\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed o
n to
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[]\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b
e a list of ar-gu-ments to be sup-plied to
[2807]
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[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
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[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2808]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
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[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2809] [2810] [2811]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7918--7918
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
Underfull \hbox (badness 1436) in paragraph at lines 7973--7979
[]\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
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 8531--8534
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super
pose
Underfull \hbox (badness 10000) in paragraph at lines 8531--8534
[]\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
[2820] [2821]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8706--8706
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
[2822]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8719--8719
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
Underfull \hbox (badness 3118) in paragraph at lines 8738--8741
[]\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
[2823]
Underfull \hbox (badness 1515) in paragraph at lines 8814--8818
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2824] [2825]
Underfull \hbox (badness 6316) in paragraph at lines 8920--8925
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2826]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 9030--9030
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2827] [2828]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9169--9169
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2829]
Underfull \hbox (badness 1028) in paragraph at lines 9228--9232
\T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r
ight.x, right.y, left.name, right.x.name,
[2830] [2831] [2832] [2833] [2834] [2835] [2836]
Underfull \hbox (badness 7238) in paragraph at lines 9692--9696
[]\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1
0 , []\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 10000) in paragraph at lines 9692--9696
[]\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4
57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 ,
[2837] [2838] [2839]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9923 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2840] [2841] [2842]
Underfull \hbox (badness 10000) in paragraph at lines 10085--10090
\T1/pcr/m/n/10 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 , []\T1/pcr/m/n/10 He
art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10158--10158
[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2843] [2844]) (./mgcv-pkg.tex
Chapter 24.
[2845] [2846]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 160--160
[]\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 163--163
[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2847]
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[] \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 184--188
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2848] [2849] [2850] [2851]
Underfull \hbox (badness 10000) in paragraph at lines 379--386
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\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 379--386
[][][]\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 379--386
[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2852]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 422--422
[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2853] [2854] [2855]
Underfull \hbox (badness 2922) in paragraph at lines 634--635
[]\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog"
[]\T1/ptm/m/n/10 and
[2856] [2857]
Underfull \hbox (badness 1406) in paragraph at lines 704--705
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2858] [2859]
Underfull \hbox (badness 1158) in paragraph at lines 814--816
[]\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
[2860]
Underfull \hbox (badness 1259) in paragraph at lines 877--878
[]\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).
[2861]
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[2863] [2864] [2865] [2866] [2867] [2868] [2869]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1337--1337
[]\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 1338--1338
[]\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 (9.78043pt too wide) in paragraph at lines 1355--1355
[] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1367--1367
[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1376--1376
[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1378--1378
[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 1409--1409
[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
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[2872]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1503--1503
[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542
[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
[2874] [2875] [2876] [2877] [2878] [2879]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1937--1937
[]\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di
screte=TRUE)[]
[2880] [2881] [2882] [2883]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2162--2162
[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2884] [2885] [2886] [2887] [2888] [2889] [2890]
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
Underfull \hbox (badness 1728) in paragraph at lines 2579--2582
[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n
/10 formula.gam[][][] []\T1/ptm/m/n/10 and also
Underfull \hbox (badness 1142) in paragraph at lines 2592--2596
\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 2618--2624
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2891] [2892] [2893]
Underfull \hbox (badness 1043) in paragraph at lines 2787--2793
\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
[2894] [2895]
Underfull \hbox (badness 10000) in paragraph at lines 2923--2929
[][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\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
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2896]
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[]\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1
e-07, maxit = 200,
[2902] [2903] [2904] [2905] [2906] [2907]
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[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
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[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
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[] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU
LL,...)[]
[2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915]
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[]\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
[2916] [2917]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[] \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)+[]
[2928] [2929] [2930]
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[]\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0,
d1b = 0,
[2931] [2932]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2933]
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[]\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver-
gence fail-ures, con-sider mod-i-fy-ing
[2934] [2935]
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[][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor
-re-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 ,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n
egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1
0 ,[][][]\T1/pcr/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 .
[2936]
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[2938] [2939] [2940]
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[]\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
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2941] [2942] [2943] [2944] [2945] [2946] [2947]
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(..
.,fit=FALSE) []\T1/ptm/m/n/10 or
[2948] [2949]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
[2950]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
[2951] [2952]
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[] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[]
[2953] [2954] [2955] [2956] [2957]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
[2958]
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[]\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[2963] [2964]
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[]\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE)
[2965] [2966] [2967] [2968]
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2982] [2983]
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2984] [2985]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[2998] [2999] [3000] [3001] [3002] [3003]
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[3005]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim
.pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd
Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p
dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 .
[3006]
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[]\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p
dTens[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n
ot nor-mally be
[3007] [3008] [3009]
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[]
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[] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[]
[3010] [3011] [3012]
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[]\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
[3013] [3014] [3015] [3016]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,gc.level=0,...)[]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para-
[3017] [3018] [3019]
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
[3020] [3021]
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[]\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi
nal grid points[]
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[]\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1)
,x3=rep(0,n))[]
[3022]
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[] \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[]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\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
[3025]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
[3026]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al
-though 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,
[3027] [3028] [3029]
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[]\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,
[3030] [3031] [3032] [3033] [3034]
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[]\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
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\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: see
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n
/10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1
/ptm/m/n/10 can be used:
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\T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s
mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[3035]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[]
[3036]
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[]\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 ,
[3037] [3038] [3039] [3040] [3041]
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[]\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)
[3042] [3043] [3044] [3045] [3046] [3047]
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[] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
+ (eps/del))[]
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[]\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[]
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[3049]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
model ma-trix X, or, if
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[]\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE,
cov = TRUE,[]
[3050]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
[3051] [3052] [3053]
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[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
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[]\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
[3054]
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\T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10
vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n
/10 "NA"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 12208--12220
[]\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w
ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec
[3055]
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[]\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able
. Plot meth-ods can be
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\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc
r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 ,
[3056] [3057] [3058]
Underfull \hbox (badness 6876) in paragraph at lines 12420--12426
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on
e or two vari-ables, spec-i-fied via terms like
[3059]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3060] [3061]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3062]
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[] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12645--12645
[] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[]
[3063]
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[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
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[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
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[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
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[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[3064]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 12738--12740
\T1/ptm/m/n/10 term []\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
[3065] [3066]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3067] [3068]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12949--12949
[]\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 12950--12950
[]\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[]
[3069] [3070]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3071] [3072] [3073] [3074] [3075]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13353--13353
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3076]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3077] [3078]
Underfull \hbox (badness 10000) in paragraph at lines 13573--13576
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met
hod a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 13573--13576
\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 13573--13576
[]\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"
[3079] [3080]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13659--13659
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3081]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 13704--13710
[]\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-
[3082] [3083] [3084]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13918--13918
[]\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...[]
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Underfull \vbox (badness 10000) has occurred while \output is active [3086]
Underfull \hbox (badness 10000) in paragraph at lines 14021--14029
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th
e sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14047--14048
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3087] [3088] [3089]
Underfull \hbox (badness 7613) in paragraph at lines 14192--14195
[]\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [
]\T1/ptm/m/n/10 pro-duced by the
[3090]
Underfull \hbox (badness 1546) in paragraph at lines 14213--14214
[]\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a
sin-gle smooth-ing pa-ram-e-
Overfull \hbox (128.58029pt too wide) in paragraph at lines 14259--14259
[]\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs
="sz",id=1),data=dat,method="REML")[]
[3091] [3092] [3093]
Underfull \hbox (badness 3396) in paragraph at lines 14405--14408
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an
y num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14450--14452
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3094] [3095] [3096] [3097] [3098] [3099]
Underfull \hbox (badness 10000) in paragraph at lines 14741--14743
[]\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see
Underfull \hbox (badness 10000) in paragraph at lines 14771--14775
[][][]\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 14771--14775
[][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 soap[][][
][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical.Spline[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14771--14775
[][][]\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 ,
[3100] [3101] [3102] [3103] [3104]
Underfull \hbox (badness 2158) in paragraph at lines 15061--15061
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3105] [3106]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15140--15140
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3107] [3108]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 15274--15274
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3109] [3110]
Underfull \hbox (badness 4846) in paragraph at lines 15405--15408
[]\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
[3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121]
[3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130]
Overfull \hbox (120.78088pt too wide) in paragraph at lines 16623--16623
[]\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL,
unconditional=FALSE, ...)[]
[3131]
Underfull \hbox (badness 1715) in paragraph at lines 16645--16646
[]\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object
$Vc []\T1/ptm/m/n/10 (if avail-able) from a
[3132] [3133] [3134]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 16835--16835
[]\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1,
Overfull \hbox (48.78088pt too wide) in paragraph at lines 16837--16837
[]\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16839--16839
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 16859--16860
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 16859--16860
[]\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le
cted by []\T1/pcr/m/n/10 ar.row
[3136]
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[3138]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17047--17047
[]\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 17048--17048
[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
[3139]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17060--17060
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[3140] [3141] [3142]) (./nlme-pkg.tex
Chapter 25.
[3143]
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
- fit-ted) are used; else, if
[3144]
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
- fit-ted) are used; else, if
[3145] [3146] [3147] [3148] [3149]
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,[]
[3150] [3151]
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 ---------------------------
---------------[]
[3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159]
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[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
[3160]
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
.htm[]\T1/ptm/m/n/10 ', the first edi-tion of
[3161] [3162] [3163] [3164] [3165] [3166] [3167]
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.
effects.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
,
[3168]
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
[3169] [3170] [3171] [3172] [3173]
Underfull \hbox (badness 2042) in paragraph at lines 1996--2002
\T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10
group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 ,
[3174]
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[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[3175]
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[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3176] [3177]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR
MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 ,
[3178]
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[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186]
Underfull \hbox (badness 10000) in paragraph at lines 2849--2853
[][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor
Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[
][][][]\T1/ptm/m/n/10 ,
[3187] [3188] [3189] [3190] [3191] [3192pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d
uplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE)
] [3193] [3194] [3195]
[3196] [3197] [3198]
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[][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau
s[][][][]\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 corSp
her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T
1/ptm/m/n/10 ,
[3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209]
[3210] [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220]
[3221] [3222]
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[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p
cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 ,
[3223] [3224] [3225] [3226] [3227] [3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5597--5600
[][][]\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 ,
[3230] [3231] [3232] [3233] [3234] [3235] [3236] [3237] [3238]
Underfull \hbox (badness 2799) in paragraph at lines 6103--6109
\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
[3239]
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[]\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 ,
[3240]
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[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl
sControl[][][][]\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 ,
[3241]
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3242] [3243] [3244] [3245]
Underfull \hbox (badness 7133) in paragraph at lines 6566--6570
[]\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 ,
[3246]
Underfull \hbox (badness 10000) in paragraph at lines 6665--6671
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn
lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6692--6692
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3247]
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3248] [3249] [3250] [3251]
Underfull \hbox (badness 10000) in paragraph at lines 7002--7009
[][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl
y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff
GroupedData[][][][]\T1/ptm/m/n/10 ,
[3252]
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[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
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[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
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[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr
oupedData []\T1/ptm/m/n/10 ob-ject or a
[3253] [3254] [3255]
Underfull \hbox (badness 10000) in paragraph at lines 7262--7267
[][][]\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 Initi
alize.glsStruct[][][][]\T1/ptm/m/n/10 ,
[3256] [3257] [3258]
Underfull \hbox (badness 1997) in paragraph at lines 7414--7422
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-tion and op-ti-
Underfull \hbox (badness 2205) in paragraph at lines 7414--7422
\T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n
/10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20,
Underfull \hbox (badness 3118) in paragraph at lines 7437--7440
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ
e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/
n/10 ,
[3259] [3260] [3261]
Underfull \hbox (badness 3354) in paragraph at lines 7653--7655
[]\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
[3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269]
Underfull \hbox (badness 10000) in paragraph at lines 8170--8187
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm
e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8170--8187
[][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL
ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\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 8213--8213
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
[3270]
Underfull \hbox (badness 1642) in paragraph at lines 8222--8244
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3271] [3272] [3273] [3274]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8487--8487
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8535--8537
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3275]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8579--8579
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286]
[3287]
Underfull \hbox (badness 10000) in paragraph at lines 9336--9343
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9347--9347
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3288] [3289] [3290] [3291] [3292]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9698 ...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
<to be read again>
\relax
l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3293]
Underfull \hbox (badness 10000) in paragraph at lines 9718--9721
[]\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 9762--9765
[]\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 9762--9765
\T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10
. Must have the same di-men-sions as
[3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] [3304]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10442--10442
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3305]
Underfull \hbox (badness 1596) in paragraph at lines 10471--10497
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3306] [3307] [3308]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10647--10647
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3309] [3310]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10798--10798
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10809--10814
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi
nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [
][][]\T1/pcr/m/n/10 nlm[][][]
[3311]
Underfull \hbox (badness 6961) in paragraph at lines 10831--10835
[]\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p
tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control=
Underfull \hbox (badness 10000) in paragraph at lines 10850--10852
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3312] [3313] [3314] [3315]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11141--11141
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11142--11142
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
[3316] [3317] [3318] [3319] [3320] [3321]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11532--11532
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3322] [3323] [3324] [3325] [3326] [3327]
Underfull \hbox (badness 6268) in paragraph at lines 11919--11929
[][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\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[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 ,
[3328] [3329] [3330] [3331]
Underfull \hbox (badness 10000) in paragraph at lines 12180--12186
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 ,
[3332] [3333] [3334] [3335] [3336]
Underfull \hbox (badness 6876) in paragraph at lines 12502--12504
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/
10 ini-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
[3337] [3338]
Underfull \hbox (badness 2452) in paragraph at lines 12658--12665
[][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\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 ,
[3339]
Underfull \hbox (badness 10000) in paragraph at lines 12723--12729
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 ,
[3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13312--13312
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3349] [3350] [3351] [3352] [3353]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13677--13677
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3354]
Underfull \hbox (badness 10000) in paragraph at lines 13704--13707
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3355]
Underfull \hbox (badness 1838) in paragraph at lines 13747--13754
[]\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 13747--13754
[]\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
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13804--13804
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3356]
Underfull \hbox (badness 10000) in paragraph at lines 13811--13814
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13811--13814
[]\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary
co-vari-ate and a sin-gle
[3357]
Underfull \hbox (badness 10000) in paragraph at lines 13919--13922
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped
Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3358] [3359]
Underfull \hbox (badness 10000) in paragraph at lines 14013--14015
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c
ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe
dData[][][][]\T1/ptm/m/n/10 ,
[3360] [3361] [3362] [3363] [3364] [3365] [3366] [3367]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14537--14537
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3368] [3369] [3370] [3371] [3372] [3373] [3374] [3375] [3376]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been
already used, duplicate ignored
<to be read again>
\relax
l.15190 ...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
<to be read again>
\relax
l.15190 ...Extract Random Effects}{random.effects}
[3377] [3378] [3379]
[3380] [3381] [3382] [3383] [3384] [3385] [3386]
Underfull \hbox (badness 2126) in paragraph at lines 15830--15834
[]\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199
7). Phar-ma-coki-net-
[3387]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15838--15838
[]\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15857--15857
[] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718
4, tol = 1.5e-5),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15858--15858
[] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),
tol = 7e-7)[]
[3388]
Underfull \hbox (badness 1009) in paragraph at lines 15888--15897
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3389] [3390]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16035--16035
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3391] [3392] [3393] [3394] [3395]
Underfull \hbox (badness 10000) in paragraph at lines 16370--16376
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l
me[][][][]\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.reStruct[][][][]\T1/ptm/m/n/10 ,
[3396]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16401--16401
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3397] [3398] [3399] [3400] [3401] [3402] [3403]
Underfull \hbox (badness 1728) in paragraph at lines 16889--16892
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3404] [3405] [3406] [3407] [3408]
Underfull \hbox (badness 1803) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite,
Underfull \hbox (badness 10000) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p
dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General
Underfull \hbox (badness 7888) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[
]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object)
[3409]
Underfull \hbox (badness 10000) in paragraph at lines 17294--17295
[]\T1/pcr/m/n/10 "Constant plus power of variance
Underfull \hbox (badness 10000) in paragraph at lines 17295--17296
[]\T1/pcr/m/n/10 "Constant plus proportion of variance
[3410] [3411] [3412] [3413]
Underfull \hbox (badness 10000) in paragraph at lines 17545--17553
[][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo
nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p
tm/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 ,
[3414] [3415] [3416] [3417]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17817--17817
[]\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17819--17819
[]\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[]
[3418] [3419] [3420] [3421] [3422] [3423]
Underfull \hbox (badness 10000) in paragraph at lines 18255--18265
[][][]\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.co
rLin[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18255--18265
[][][]\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 Variogr
am.corSpher[][][][]\T1/ptm/m/n/10 ,
[3424]
Underfull \hbox (badness 3579) in paragraph at lines 18293--18298
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3425]
Underfull \hbox (badness 3579) in paragraph at lines 18357--18362
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3426]
Underfull \hbox (badness 3579) in paragraph at lines 18420--18425
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3427]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR
atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3428]
Underfull \hbox (badness 3579) in paragraph at lines 18546--18551
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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[][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va
riogram[][][][]\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 18579--18588
[][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rRatio[][][][]\T1/ptm/m/n/10 ,
[3429]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3430] [3431]
Underfull \hbox (badness 1009) in paragraph at lines 18764--18773
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3432] [3433]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again>
\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
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\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3443]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3444] [3445] [3446]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3447]
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[]\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)),[]
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[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3448] [3449]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3450]) (./rpart-pkg.tex
Chapter 27.
[3451] [3452] [3453] [3454]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3455] [3456] [3457] [3458]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil
l be at the hor-i-zon-tal plot co-or-di-nates of
[3459] [3460]
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[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
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[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
adds to the la-bel
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\T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [
]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n
[3461] [3462] [3463]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
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[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"),[]
[3464] [3465] [3466] [3467]
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[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
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[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
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[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n
/10 rpart []\T1/ptm/m/n/10 al-go-rithm. See
[3468]
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[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
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[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3469] [3470] [3471] [3472] [3473] [3474] [3475]
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[]\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 ',
[3476]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3477] [3478] [3479]) (./spatial-pkg.tex [3480]
Chapter 28.
[3481] [3482] [3483] [3484] [3485] [3486]
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[3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497]
[3498] [3499]) (./survival-pkg.tex [3500]
Chapter 29.
[3501] [3502]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
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[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3503] [3504]
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[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as
long as
[3505] [3506]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again>
\relax
l.384 ... 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
<to be read again>
\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
[3507]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
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[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3508]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3509] [3510] [3511]
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[]\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival
[3512]
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3513] [3514]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3515] [3516] [3517]
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
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[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3518] [3519]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1241--1241
[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3520]
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[]\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter,
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.1308 ...erapy for Stage B/C colon cancer}{colon}
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[] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[]
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[] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[]
[3522] [3523] [3524]
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[] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3525] [3526] [3527] [3528] [3529]
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[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
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\T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T
1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe-
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\T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv
(time, status) ~ age +
[3530]
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[][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][]
[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\
T1/ptm/m/n/10 ,
[3531]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3532] [3533] [3534] [3535] [3536] [3537] [3538] [3539]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717
[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3540]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3541] [3542] [3543]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3544] [3545] [3546]
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[3548]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3549]
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[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
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[]\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
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[] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[]
[3550] [3551]
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[] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3552] [3553]
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[] []
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[3555]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3556] [3557] [3558] [3559] [3560] [3561] [3562]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4210--4210
[] \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 )))[]
[3563] [3564]
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[]\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[]
[3565]
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[]\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[]
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[]\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2:
4] - yhat[1][]
[3566] [3567]
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[3569] [3570] [3571]
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[] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[]
[3572] [3573] [3574]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3575] [3576]
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[]\T1/pcr/m/n/9 mresid <- (lung$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[]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3577]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3578]
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[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[]
[3579]
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[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt
m/m/n/10 , which is the re-sult of the
[3580] [3581] [3582]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5512--5512
[]\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1
=FALSE, ...)
[3583]
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[]\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2
), se.fit=TRUE)[]
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[]\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval
ues smooth it.[]
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[]\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g
., svyglm, but[]
[3584]
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[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
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[] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[]
[3585] [3586]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3587]
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[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
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[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
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[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3588] [3589] [3590] [3591] [3592] [3593] [3594]
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[] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[]
[3595] [3596] [3597]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
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[]\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp
"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and
[3598] [3599] [3600] [3601] [3602]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[]
[3603] [3604]
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[]\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE)
[3605]
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[]\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem
ove duplicate times[]
[3606]
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[]\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times=
365*c(3, 5))[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.7224 ...ata from a soldering experiment}{solder}
[3607]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3608] [3609] [3610] [3611] [3612] [3613]
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[]\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[]
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[]\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[]
[3614] [3615] [3616] [3617]
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[] \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 ),[]
[3618] [3619] [3620] [3621]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods
first con-struct a sur-vival curve us-ing
[3622] [3623]
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[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3624] [3625] [3626]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
[3627]
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[]\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre
-dicted sur-vival
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3628]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3629] [3630] [3631] [3632]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10
,
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[] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
ctype,[]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
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[] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2
, ctype,[]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
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[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3636]
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\T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a-
lent to []\T1/pcr/m/n/10 stype=2,
[3637] [3638]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3639] [3640] [3641] [3642] [3643]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3644]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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[]\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) #
use concordance
[3645] [3646] [3647]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su
rvreg.distributions[][][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T
1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p
tm/m/n/10 ,
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[]\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, i
t is
[3648]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3649]
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[3650] [3651]
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[] \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 )[]
[3652]
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[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
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[] \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 )[]
[3653] [3654] [3655]
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[]\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100
0, data=test)[]
[3656] [3657]
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[]\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[]
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[]\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
set has data[]
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[] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[]
[3658] [3659] [3660] [3661] [3662] [3663] [3664]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3665] [3666] [3667]) [3668] (./fullrefman.ind [3669] [3670] [3671] [3672]
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.sz.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
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[3739]
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[3748]
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[]\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method
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[3749] [3750] [3751]
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[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method
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[]\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method
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[]\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method
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[]\T1/pcr/m/n/10 norm,denseMatrix,character-method
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[]\T1/pcr/m/n/10 norm,sparseMatrix,character-method
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[]\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method
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[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method
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[3804]
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[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,dgeMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method
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Chapter 1.
[3] [4]
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[]\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 []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/
n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth
-er-wise, it is []\T1/pcr/m/n/10 (double.base ^
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[]\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 . It
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\T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T
1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base
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[]\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, it is []\T1/pcr/m/n/10 (double.base
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\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p
cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As
[5]
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[]\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p
tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel
y anal-o-gously to their
[6] [7]
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[][][]\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-l
ar,
[8] [9] [10]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
[11]
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[]\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v
alue = TRUE)[]
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[]\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i
gnore.case = TRUE)[]
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[]\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9)
# "absolute"[]
[16]
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[]\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean
rel.diff.=",[]
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[26] [27]
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[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
[28]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
than 256 (or
[29] [30] [31] [32]
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[]\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[]
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[]\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is
true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which
an
[33] [34] [35] [36]
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[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
[37]
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[] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo
ne1970.tab"),[]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n
/10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[40] [41]
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2,
lwd = 1, bty="n")[]
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[]\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
[52]
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[]\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
"", type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[59] [60] [61] [62] [63] [64] [65] [66]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
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\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 o
r
[67]
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
[68]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
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[]\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
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[]\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 []\T1/pcr/m/n/10 c("first",
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[]\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 : / /
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\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}[]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n
/10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\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
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[]\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
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
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[]\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de
fault", "internal",
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[]\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 ,
[104] [105] [106]
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri
ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n
/10 only. This
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\T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http
s : / / specifications . freedesktop .
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[]\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion
as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys-
[107] [108]
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Underfull \vbox (badness 10000) has occurred while \output is active [110]
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[111] [112] [113] [114]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[115] [116] [117]
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/pcr/m/n/9 ## curlGetHeaders("ftp://cran.r-project.org") ## ftp::// suppo
rt is vanishing[]
[118] [119] [120] [121]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[122]
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[]\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
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[][][]\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
[123] [124] [125]
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[] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[]
[126] [127] [128] [129]
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\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 , and
[130] [131] [132] [133] [134] [135]
Underfull \hbox (badness 10000) in paragraph at lines 9291--9295
[]\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions.
Func-tions should be listed in
[136] [137]
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[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
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[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[138] [139]
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[]\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha
racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b
y
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m
/n/10 formula[][][][]\T1/ptm/m/n/10 s, with
[140] [141] [142]
Underfull \hbox (badness 1603) in paragraph at lines 9794--9797
[]\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
[143] [144] [145] [146] [147] [148] [149] [150] [151]
Underfull \hbox (badness 1917) in paragraph at lines 10410--10415
[]\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10
dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[152]
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[153] [154]
Underfull \hbox (badness 1168) in paragraph at lines 10568--10573
[]\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\
T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by
[155]
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[]\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n
ames(list(...));[]
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[]\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()),
names(list(...))))[]
[156] [157]
Underfull \hbox (badness 2828) in paragraph at lines 10791--10796
[][][]$\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 .
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\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 / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / /
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[158]
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[]\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[]
[159] [160]
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[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[161] [162] [163]
Underfull \hbox (badness 6396) in paragraph at lines 11242--11250
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
Underfull \hbox (badness 10000) in paragraph at lines 11251--11253
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len
t to but faster than
[164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 11468--11471
[]\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D
LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use
[167] [168] [169] [170] [171] [172]
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[]\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma
y lead to con-fu-sion (see
[173]
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[]\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[]
[174] [175] [176]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1
0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt
m/m/n/10 and
[177]
Underfull \hbox (badness 10000) in paragraph at lines 12246--12249
[]\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used
by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if
Underfull \hbox (badness 10000) in paragraph at lines 12264--12266
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[178] [179] [180] [181]
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc
r/m/n/10 where []\T1/ptm/m/n/10 as
Underfull \hbox (badness 5970) in paragraph at lines 12557--12559
[]\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/10 is true, oth-er-wise
[182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13375--13375
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[194] [195] [196] [197] [198] [199] [200] [201] [202] [203]
Underfull \hbox (badness 2253) in paragraph at lines 14100--14102
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
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[]\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m
a-tion is given about the
[204] [205]
Underfull \hbox (badness 2573) in paragraph at lines 14268--14270
[]\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
[]\T1/pcr/m/n/10 fsep =
[206] [207]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[208] [209]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][][]\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 14559--14562
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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[] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B
as it exists already[]
[210]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[211]
Underfull \hbox (badness 10000) in paragraph at lines 14702--14705
[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.exists[][][][]\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 14712--14712
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[212]
Underfull \hbox (badness 10000) in paragraph at lines 14778--14781
[]\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d
i-tion ob-ject of class
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[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
[213]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
Underfull \hbox (badness 3965) in paragraph at lines 14856--14860
[]\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,
[214] [215] [216]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15020--15020
[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15021--15021
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[217] [218] [219] [220]
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[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
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[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
[221]
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[]\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-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
[222]
Underfull \hbox (badness 6944) in paragraph at lines 15449--15452
[][][]\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/1
0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 ,
[223]
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[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[224] [225]
Underfull \hbox (badness 10000) in paragraph at lines 15612--15614
[]\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p
os-si-bly for-mat-ted) num-bers, also in
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[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
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[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[]
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[]\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
[226]
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[]\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
[227]
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[]\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 ,
which calls []\T1/pcr/m/n/10 .format.zeros(*,
Underfull \hbox (badness 10000) in paragraph at lines 15773--15778
[]\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call
s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri
des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10
formatC(123.45, mode =
Underfull \hbox (badness 10000) in paragraph at lines 15790--15798
[]\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
[228] [229]
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[]\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 ")[]
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[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
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[231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16754--16754
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[242] [243]
Underfull \hbox (badness 2418) in paragraph at lines 16863--16867
\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/pt
m/m/n/10 ,
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s
ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR
UE[]\T1/ptm/m/n/10 , then the sin-gle
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[][][]\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[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][]
\T1/ptm/m/n/10 ,
[244] [245]
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[]\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/
ptm/m/n/10 calls C level
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[]\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose
of flush-ing (i.e., emp-ty-ing) the
[246]
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[]\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f
actory" default[]
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[]\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if
translation works)[]
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[]\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex
ample started:[]
[248] [249]
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[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[250] [251] [252] [253]
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[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
[254]
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[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active [255]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17660--17660
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
[256] [257] [258] [259]
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[]\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)))
[260]
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[]\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[]
[261] [262] [263]
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[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[264] [265] [266] [267] [268]
Underfull \hbox (badness 1163) in paragraph at lines 18653--18655
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 https : / / unicode-[]org . github . io / icu /
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[]\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.[]
[269]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[270]
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[] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se
t = FALSE,[]
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[] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F
ALSE,[]
[271]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
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[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
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[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
[272] [273]
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[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
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[]\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[]
[274] [275] [276]
Underfull \hbox (badness 10000) in paragraph at lines 19194--19196
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T
1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and
[277] [278] [279] [280] [281]
Underfull \hbox (badness 10000) in paragraph at lines 19532--19538
Underfull \hbox (badness 10000) in paragraph at lines 19545--19547
[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[282] [283] [284]
Underfull \hbox (badness 4699) in paragraph at lines 19777--19780
[]\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty
pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 ,
[285] [286]
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[287] [288] [289]
Underfull \hbox (badness 4739) in paragraph at lines 20040--20042
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[290]
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[]\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co
lumn names differ)[]
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[]\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are
not checked)[]
[291] [292] [293] [294] [295] [296] [297] [298] [299]
Underfull \hbox (badness 1975) in paragraph at lines 20709--20712
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[300] [301] [302] [303] [304] [305]
Underfull \hbox (badness 1077) in paragraph at lines 21124--21129
[]\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st
al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T
1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 21138--21145
[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
[306]
Underfull \hbox (badness 1112) in paragraph at lines 21212--21221
[]\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the
en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 ,
[307]
Underfull \hbox (badness 2970) in paragraph at lines 21272--21275
[]\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us
ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a
Underfull \hbox (badness 2951) in paragraph at lines 21272--21275
\T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It
may be opened by
[308] [309]
Underfull \hbox (badness 10000) in paragraph at lines 21385--21389
[]\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 21385--21389
[][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi
s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 21390--21397
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no
[]\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m
/n/10 ar-gu-ment, it lists all avail-able pack-
[310] [311]
Underfull \hbox (badness 10000) in paragraph at lines 21521--21528
[][][]\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 autoloa
d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/
m/n/10 ,
[312]
Underfull \hbox (badness 10000) in paragraph at lines 21642--21646
[]\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
[313]
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
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\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 21712--21717
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 21712--21717
\T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s
ion 3 of the li-cense can be dis-played by
[314] [315] [316]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[317]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/
m/n/10 for many more file han-dling func-tions and
[318] [319]
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[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
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[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
prob = 0.2))),[]
[320] [321]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
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[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
[322] [323]
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[]\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
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[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
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[]\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war
ning messages[]
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[] \T1/pcr/m/n/9 sg <- matrix(unlist(strsplit(strsplit(Sys.getlocale(), sep)[[
1]], "=")), nrow=2)[]
[324] [325]
Underfull \hbox (badness 1400) in paragraph at lines 22575--22579
[][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[]
[][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m
/n/10 double[][][] []\T1/ptm/m/n/10 (class
[326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337]
[338]
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[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
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[] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N
aN, imaginary = r ))[]
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[]\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)[]
[339]
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[]\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE
) # |--> "abc"[]
[340]
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[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[341] [342] [343]
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[]\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 tcross
prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able.
[344] [345] [346] [347] [348] [349] [350] [351] [352]
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[]\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
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\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[353] [354]
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[355] [356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 1448) in paragraph at lines 25014--25022
[]\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a
s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive =
[363]
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[]\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-
nally to a char-ac-ter vec-tor (so meth-ods for
[364]
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[]\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-r
e-spond-ing list,
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\T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\
T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env,
Underfull \hbox (badness 3148) in paragraph at lines 25206--25212
\T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi
-ron-ment is used as a hash ta-ble,
[365] [366] [367]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1
0 c("bytes", "chars",
[368] [369] [370]
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[]\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e
ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by
[371] [372] [373]
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\T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10
and in case of an er-ror (such as in-suf-fi-cient per-
[374] [375] [376] [377]
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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[]\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti
al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use
[378]
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[]\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m
ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab
out the pack-
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\T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c
om-puted pack-age in-for-ma-tion ob-ject and pass this to
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[]\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only)
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
[379]
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[]\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space
it loads to the search path.
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[]\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram
e con-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but
more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in%
[380]
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[] \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:[]
[381] [382] [383]
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[]\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
[][]mode[][][]
[384] [385] [386]
Underfull \hbox (badness 1694) in paragraph at lines 26704--26707
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[387] [388] [389] [390]
Underfull \hbox (badness 1603) in paragraph at lines 26976--26978
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[391] [392]
Underfull \hbox (badness 1210) in paragraph at lines 27103--27111
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-
[393] [394]
Underfull \hbox (badness 3271) in paragraph at lines 27323--27326
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[395] [396]
Underfull \vbox (badness 3780) has occurred while \output is active [397]
[398]
Underfull \hbox (badness 3138) in paragraph at lines 27629--27635
[]\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 27629--27635
\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 27629--27635
\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 27642--27645
[]\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/pt
m/m/n/10 and
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[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 (and in-di-rectly
[399]
Underfull \hbox (badness 1009) in paragraph at lines 27728--27731
[]\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p
ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T
1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN
ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27752--27758
\T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1
/pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27752--27758
\T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5091) in paragraph at lines 27752--27758
[]\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma
c.binary.universal" []\T1/ptm/m/n/10 are no longer
Underfull \hbox (badness 10000) in paragraph at lines 27767--27774
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][][]\T1/pcr/m/n/10 up
date.packages[][][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 2384) in paragraph at lines 27767--27774
[]\T1/pcr/m/n/10 c(CRAN="@CRAN@")[]\T1/ptm/m/n/10 , a value that causes some ut
il-i-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 27767--27774
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke []\T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 27767--27774
\T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran";
[400] [401] [402] [403] [404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28115--28115
[]\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 28128--28132
[]\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.
y)] = FUN(X[arrayindex.x],
[405] [406]
Underfull \hbox (badness 1210) in paragraph at lines 28275--28278
[]\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la
ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex
t=s,
[407] [408] [409] [410]
Underfull \hbox (badness 7133) in paragraph at lines 28557--28563
[][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc
r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28579--28579
[]\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 28591--28591
[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
[411]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 28604--28604
[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling :
[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[]
[412] [413]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28791--28791
[]\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt
cars, cyl == 4))[]
[414]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28806--28806
[]\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so
is not evaluated[]
Underfull \hbox (badness 1360) in paragraph at lines 28861--28865
[]\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., []\T1/pcr/m/n/10 type =
[415] [416] [417] [418] [419]
Underfull \hbox (badness 2277) in paragraph at lines 29173--29178
\T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt
m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing
[420] [421]
Underfull \hbox (badness 1701) in paragraph at lines 29289--29293
[]\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/
pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\
T1/pcr/m/n/10 get[][][](name, envir =
[422]
Underfull \hbox (badness 1796) in paragraph at lines 29357--29360
[]\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i
n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed
out-put, see
[423] [424] [425]
Underfull \hbox (badness 10000) in paragraph at lines 29561--29564
[]\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p
rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[426] [427] [428] [429] [430] [431] [432] [433] [434] [435]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 30256--30256
[] \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))[]
[436] [437] [438] [439] [440]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30549--30549
[]\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 30560--30560
[]\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 30566--30566
[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
[441]
Underfull \hbox (badness 7415) in paragraph at lines 30662--30666
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v
ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
[442]
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[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 30729--30729
[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
[443] [444]
Underfull \hbox (badness 3713) in paragraph at lines 30874--30885
[]\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma
n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm
/m/n/10 (not
[445] [446]
Underfull \hbox (badness 1248) in paragraph at lines 31026--31033
\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 31026--31033
\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 /
[447]
Underfull \hbox (badness 1533) in paragraph at lines 31144--31147
[]\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
[448] [449] [450]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 31289--31289
[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N
A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[451] [452]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31451--31451
[]\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[]
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[]\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
of deparse()[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31455--31455
[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31456--31456
[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h
ow = "unlist")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 31463--31463
[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
[453] [454] [455] [456] [457]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 31771--31771
[]\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl
e prec numbers :[]
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[]\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
# split one double[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31783--31783
[]\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31784--31784
[]\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x)
numToBits(x) , raw(64L))[]
Underfull \vbox (badness 10000) has occurred while \output is active [458]
[459]
Underfull \hbox (badness 4048) in paragraph at lines 31879--31884
[]\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 31879--31884
\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 31879--31884
\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 ,
[460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 2080) in paragraph at lines 32417--32427
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/
10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n
/10 (ver-sion num-ber, cur-rently 2 or 3),
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32451--32451
[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
[468] [469] [470] [471] [472] [473] [474]
Underfull \hbox (badness 7558) in paragraph at lines 32971--32975
[]\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p
tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 32981--32983
[]\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
[475]
Underfull \hbox (badness 10000) in paragraph at lines 32992--32994
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / /
pubs . opengroup . org / onlinepubs /
Underfull \hbox (badness 1975) in paragraph at lines 32995--32999
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m
/n/10 https : / / www .
[476] [477] [478] [479] [480]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33366--33366
[]\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete
replications[]
[481]
Underfull \hbox (badness 10000) in paragraph at lines 33437--33441
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[482] [483] [484]
Underfull \hbox (badness 2302) in paragraph at lines 33663--33668
[]\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-
ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant
Underfull \hbox (badness 1824) in paragraph at lines 33663--33668
\T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/
10 round(x, dig -
[485] [486]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33796--33796
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33806--33806
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
[487] [488] [489] [490] [491] [492] [493]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34254--34254
[] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob)
&& size <= n/2))[]
[494] [495] [496] [497] [498] [499] [500]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34691--34691
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[501]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length
1, it ap-plies to all fields; oth-er-wise, if
[502] [503]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 34981--34981
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[504] [505] [506] [507]
Underfull \hbox (badness 4752) in paragraph at lines 35241--35244
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/
m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 5563) in paragraph at lines 35245--35251
[]\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
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517]
Underfull \hbox (badness 10000) in paragraph at lines 35915--35926
[]\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a
p-pli-ca-tion as well as
Underfull \hbox (badness 3271) in paragraph at lines 35915--35926
\T1/ptm/m/n/10 the shell. It may de-pend on the com-piler used: Mi-crosoft's ru
les for the C run-
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\T1/ptm/m/n/10 time are given at [][]$\T1/pcr/m/n/10 https : / / docs . microso
ft . com / en-[]us / cpp / c-[]language /
Underfull \hbox (badness 1635) in paragraph at lines 35915--35926
\T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][
]\T1/ptm/m/n/10 . It may de-pend on the
[518] [519] [520] [521] [522] [523] [524] [525]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 36455--36455
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[526] [527] [528]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36707--36707
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 36709--36709
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[529]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/
pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T
1/ptm/m/n/10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 36752--36758
[][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \
T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[530] [531]
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[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[532] [533] [534] [535] [536]
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[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[537] [538] [539]
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[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
[540] [541] [542]
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[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
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[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[543] [544] [545] [546] [547]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 38005--38005
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[548]
Underfull \hbox (badness 6110) in paragraph at lines 38101--38111
[]\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-at
e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 38101--38111
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
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\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert
a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 38101--38111
\T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages
on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 38101--38111
\T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as
an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ).
Us-ing
[549]
Underfull \hbox (badness 10000) in paragraph at lines 38157--38163
[]\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 38157--38163
\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,
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\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
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 38172--38179
\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 38172--38179
\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
[550]
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[]\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba
ckslashes in[]
[551] [552] [553]
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[]\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T
1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
[554] [555] [556] [557] [558] [559] [560]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 38955--38955
[]\T1/pcr/m/n/9 (fF <- format(.POSIXct(notF))) # was all NA, now the last is
still NA (not "NA")[]
[561] [562]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 39064--39064
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[563] [564] [565]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[566]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[567] [568] [569] [570] [571] [572] [573]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 39805--39805
[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
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[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
[574]
Underfull \hbox (badness 10000) in paragraph at lines 39859--39866
[]\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 39859--39866
[]\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form
at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m
/n/10 ).
[575]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39912--39912
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[576] [577] [578] [579]
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[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[580] [581] [582]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 40389--40389
[]\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.
[583]
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[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
Underfull \hbox (badness 2293) in paragraph at lines 40457--40463
[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 40457--40463
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call.
Underfull \hbox (badness 4792) in paragraph at lines 40476--40481
[]\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10
this may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 40476--40481
[]\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
[584] [585] [586] [587]
Underfull \hbox (badness 10000) in paragraph at lines 40764--40768
[]\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent
s []\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
[588]
Underfull \hbox (badness 1584) in paragraph at lines 40779--40782
[]\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy
s.function []\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
[589] [590]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 40917--40917
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[591]
Overfull \hbox (19.22812pt too wide) in paragraph at lines 40998--40998
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used
[592] [593]
Underfull \hbox (badness 1082) in paragraph at lines 41143--41146
[]\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions
keep their source in-clud-ing com-ments, see
[594]
Underfull \hbox (badness 10000) in paragraph at lines 41170--41172
[][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo
adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li
brary[][][](.) []\T1/ptm/m/n/10 and uses
[595] [596]
Underfull \hbox (badness 1038) in paragraph at lines 41336--41339
[]\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c
at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[597] [598] [599] [600] [601]
Underfull \hbox (badness 1442) in paragraph at lines 41701--41705
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout
= TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout =
[602] [603] [604] [605]
Underfull \hbox (badness 4096) in paragraph at lines 41955--41958
[]\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri
nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin.
table[][][][]\T1/ptm/m/n/10 ,
[606]
Underfull \hbox (badness 7888) in paragraph at lines 42069--42073
[]\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can
have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/
m/n/10 length(bin) >
[607] [608] [609]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 42223--42223
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (30.0281pt too wide) in paragraph at lines 42225--42225
[] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[]
Overfull \hbox (55.67578pt too wide) in paragraph at lines 42227--42227
[] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 =
NULL), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 42240--42242
[]\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t
hat was reg-is-tered ear-lier via
[610]
Underfull \hbox (badness 10000) in paragraph at lines 42320--42323
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[611] [612]
Underfull \hbox (badness 3872) in paragraph at lines 42438--42441
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 5475) in paragraph at lines 42504--42508
[][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback
Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[614] [615] [616] [617] [618] [619]
Underfull \hbox (badness 1655) in paragraph at lines 42927--42934
\T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[]
\T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1
/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ',
Underfull \hbox (badness 2253) in paragraph at lines 42935--42940
[]\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se
e the ex-am-ples for typ-i-cal cases. It may
Underfull \hbox (badness 1655) in paragraph at lines 42935--42940
\T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 ,
some-thing like `[]\T1/pcr/m/n/10 "2020a"[]\T1/ptm/m/n/10 '. (It does on sys-te
ms us-ing
Underfull \hbox (badness 4467) in paragraph at lines 42985--42994
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-
turns the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 42985--42994
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
[620]
Underfull \hbox (badness 1082) in paragraph at lines 42995--43007
[]\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/1
0 ' in that di-rec-tory states the ver-sion. That op-tion is
[621]
Underfull \hbox (badness 1337) in paragraph at lines 43080--43088
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
Underfull \hbox (badness 3460) in paragraph at lines 43143--43146
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 43147--43149
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
[622]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 43156--43156
[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[623] [624] [625] [626]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 43499--43499
[]\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 43501--43501
[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
[627]
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Overfull \hbox (84.78088pt too wide) in paragraph at lines 43602--43602
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 43604--43604
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
[629] [630] [631] [632]
Underfull \hbox (badness 6542) in paragraph at lines 43878--43880
[]\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 , an
d
[633]
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
[634]
Underfull \hbox (badness 1708) in paragraph at lines 44065--44073
[]\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any
er-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 44065--44073
\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
[635]
Underfull \hbox (badness 4859) in paragraph at lines 44105--44110
[][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle
rs and sup-press-ing the print-ing of er-ror mes-sages;
[636]
Underfull \hbox (badness 3895) in paragraph at lines 44167--44179
[]\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 44167--44179
\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 ,
[637] [638] [639] [640] [641]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 44490--44490
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[642] [643] [644] [645] [646] [647]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44959--44959
[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
[648]
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[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[]
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[][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc
ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n
/10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][]
\T1/ptm/m/n/10 ,
[649]
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[][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di
r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/
ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\
T1/ptm/m/n/10 ,
[650]
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[]\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[]
[651]
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[]\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\
T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ),
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[]\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
[652] [653] [654]
Underfull \hbox (badness 3668) in paragraph at lines 45432--45434
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[655]
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[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[656] [657]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 45613--45613
[]\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[]
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[]\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
There were 105 warnings ...[]
[658]
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[]\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[]
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[]\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings
AsFactors = FALSE) {[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 45720--45720
[] \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa
ctors=stringsAsFactors)[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix
- dropping time info {sec,min,hour, isdst}[]
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[]\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[]
[659]
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[]\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
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[]\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name
ly a ma-trix whose rows each
[660] [661]
Underfull \hbox (badness 2818) in paragraph at lines 45887--45893
[]\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 and []\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
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[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[662] [663] [664] [665] [666] [667] [668]
Underfull \hbox (badness 2846) in paragraph at lines 46381--46385
[]\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren
tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[669]
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[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
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[]\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da
rd' reg-exps, in-clud-ing el-e-ments named
[670]) (./compiler-pkg.tex
Chapter 2.
[671]
Underfull \hbox (badness 2884) in paragraph at lines 106--120
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b
e used to con-trol com-piler op-er-a-tion. There are cur-
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\T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef
ined[]\T1/ptm/m/n/10 , and
[672] [673] [674]) (./datasets-pkg.tex
Chapter 3.
[675] [676] [677] [678] [679]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301
[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[680]
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[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
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[682] [683] [684]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617
[] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[]
[685]
Underfull \hbox (badness 4779) in paragraph at lines 704--707
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[686] [687]
Underfull \hbox (badness 4779) in paragraph at lines 837--840
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[688] [689] [690]
Underfull \hbox (badness 1097) in paragraph at lines 1037--1041
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[691]
Underfull \hbox (badness 4779) in paragraph at lines 1152--1155
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[692] [693] [694] [695] [696]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464
[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[697] [698]
Underfull \hbox (badness 10000) in paragraph at lines 1549--1552
[]\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr
ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q
uarterly.revenue[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1549--1552
[]\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-taine
d from the above
[699] [700] [701]
Underfull \hbox (badness 4779) in paragraph at lines 1738--1741
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[702]
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[]\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 1840--1840
[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[703] [704]
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[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
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[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[705] [706] [707] [708]
Underfull \hbox (badness 4779) in paragraph at lines 2160--2163
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[709] [710] [711]
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[712] [713] [714] [715] [716]
Underfull \hbox (badness 4779) in paragraph at lines 2725--2728
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[717]
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[718]
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[720] [721] [722] [723]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[724] [725] [726] [727] [728] [729] [730] [731]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3611--3611
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[732] [733]
Underfull \hbox (badness 4779) in paragraph at lines 3759--3762
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[734]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[735]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[736]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
Underfull \hbox (badness 10000) in paragraph at lines 4006--4008
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
Underfull \hbox (badness 10000) in paragraph at lines 4006--4008
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750]) (./grDevices-pkg.tex
Chapter 4.
[751] [752] [753] [754]
Underfull \hbox (badness 4752) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/
ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p
tm/m/n/10 in
[755] [756] [757] [758]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[759] [760] [761] [762] [763] [764] [765] [766] [767] [768]
Underfull \hbox (badness 5175) in paragraph at lines 1192--1194
[]\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
[769] [770] [771]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363
[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[772] [773] [774]
Underfull \hbox (badness 3302) in paragraph at lines 1624--1628
[]\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo
re of
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[]\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern")
[775] [776] [777] [778] [779]
Underfull \hbox (badness 1565) in paragraph at lines 1914--1919
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i
s to pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1914--1919
\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
[780]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[781]
Underfull \hbox (badness 1184) in paragraph at lines 2038--2048
[]\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 2038--2048
[]\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp
ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 ,
[782]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[783] [784] [785]
Underfull \hbox (badness 6758) in paragraph at lines 2329--2332
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[786] [787]
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[]\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se
tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place
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\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
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\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 2447--2457
[]\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10
setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics
[788]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[789] [790]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2666--2666
[]\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)
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[]\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[]
[791] [792] [793] [794]
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[796] [797] [798] [799]
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[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[800]
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[]\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 3358--3358
[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[801] [802] [803]
Underfull \hbox (badness 10000) in paragraph at lines 3516--3522
[]\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b
ased on the inter-quartile range
[804]
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[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[]
[805]
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[]\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[]
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[]\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[]
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[] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab =
"", main=main)[]
[806]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
[807]
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[]\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 ,
[808]
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[]\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work
s well for shad-ing points or lines in up to five groups,
Underfull \hbox (badness 10000) in paragraph at lines 3886--3890
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[809]
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[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10
give a C in-te-ger for-mat such as
[811] [812] [813] [814] [815]
Underfull \hbox (badness 5939) in paragraph at lines 4349--4354
[]\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 family[]\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 ,
[816] [817] [818] [819] [820] [821] [822] [823]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4869--4869
[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[824] [825]
Underfull \hbox (badness 1348) in paragraph at lines 5074--5077
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[826]
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024,
height = 768)[]
Underfull \hbox (badness 7522) in paragraph at lines 5139--5145
[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10
give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as
[827]
Underfull \hbox (badness 1112) in paragraph at lines 5172--5176
[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), []\T1/pcr/m/n/10 "CP1251.enc"
[828]
Underfull \hbox (badness 1755) in paragraph at lines 5314--5316
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[829] [830] [831]
Underfull \hbox (badness 7344) in paragraph at lines 5494--5496
[]\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 5505--5509
[][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][]
[]\T1/ptm/m/n/10 which is called from both
[832] [833]
Underfull \hbox (badness 1552) in paragraph at lines 5632--5641
[]\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 "He
lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal
atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc
r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\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/p
cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2221) in paragraph at lines 5642--5644
[]\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and
Underfull \hbox (badness 4686) in paragraph at lines 5674--5680
[]\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p
cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for
[834]
Underfull \hbox (badness 5388) in paragraph at lines 5700--5702
[]\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p
cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
[835] [836]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803
[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[837]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5915--5915
[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
[838] [839]
Underfull \hbox (badness 10000) in paragraph at lines 6001--6003
[]\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][]
\T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T
1/ptm/m/n/10 for on-screen de-vices and to
[840] [841] [842] [843] [844]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6368--6368
[]\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 6382--6385
[]\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r
ed/green/blue) into HSV space
[845] [846] [847] [848] [849] [850]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6717--6717
[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6724--6724
[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
[851] [852] [853] [854]
Underfull \hbox (badness 10000) in paragraph at lines 6990--6995
[]\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 pointsize[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10
,
Underfull \hbox (badness 1803) in paragraph at lines 6990--6995
[]\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/
ptm/m/n/10 ,
Underfull \hbox (badness 2941) in paragraph at lines 6990--6995
[]\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi
rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
fillOddEven []\T1/ptm/m/n/10 and
[855]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7096--7096
[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
[856]
Underfull \hbox (badness 3590) in paragraph at lines 7135--7138
[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 2393) in paragraph at lines 7135--7138
\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
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[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
[857]
Underfull \hbox (badness 1189) in paragraph at lines 7211--7213
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[858]
Underfull \hbox (badness 10000) in paragraph at lines 7316--7318
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ
K lan-guages and
[859]
Underfull \hbox (badness 10000) in paragraph at lines 7362--7369
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of []
\T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2469) in paragraph at lines 7362--7369
[]\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu
x sys-tems which have the Wine
[860]
Underfull \hbox (badness 5607) in paragraph at lines 7446--7450
[]\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d
o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and
[861]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7498--7498
[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[862] [863]
Underfull \hbox (badness 5637) in paragraph at lines 7630--7636
[]\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 7663--7666
[]\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 /
[864] [865] [866]
Underfull \hbox (badness 1231) in paragraph at lines 7832--7834
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10
number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of
[867] [868]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 4647) 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 []\T1/pcr/m/n/10 library(help =
[869] [870] [871] [872] [873] [874] [875]
Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450
[] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[]
Underfull \hbox (badness 4048) in paragraph at lines 482--488
[]\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
[876] [877]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580
[]\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[]
[878]
Underfull \hbox (badness 10000) in paragraph at lines 694--698
[]\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 694--698
[][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T
1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\
T1/ptm/m/n/10 if
[879] [880]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 770--770
[]\T1/pcr/m/n/9 ## 1e-01 1e+01 1e+03 1e+05 1e+07 1e+09 1e+11 ; since R 4.2.0:
1e-2 1e0 1e2 .. 1e10[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 782--782
[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 819--819
[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
[881] [882] [883]
Underfull \hbox (badness 10000) in paragraph at lines 966--970
[][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1
/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl
e.
Overfull \hbox (133.98029pt too wide) in paragraph at lines 983--983
[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 985--985
[]\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset
= Age=="Adult"))[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 987--987
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
[884] [885] [886] [887]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1271--1271
[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
[888] [889] [890]
Underfull \hbox (badness 2503) in paragraph at lines 1433--1442
\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and
[]\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3375) in paragraph at lines 1468--1470
[]\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt
m/m/n/10 ),
[891] [892]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1542--1542
[]\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 1543--1543
[]\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 1549--1549
[]\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 1550--1550
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[893] [894] [895] [896] [897]
Underfull \hbox (badness 10000) in paragraph at lines 1853--1859
[][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr
/m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1873--1873
[]\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1885--1885
[]\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1901--1901
[]\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 1910--1910
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
[898] [899]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1995--1995
[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[900] [901]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2124--2124
[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2129--2129
[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
[902] [903]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2303--2303
[]\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 2304--2304
[] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[]
[904]
Underfull \hbox (badness 1430) in paragraph at lines 2335--2337
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10
"n" []\T1/ptm/m/n/10 to sup-press and see also
[905]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2416--2416
[] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[]
Underfull \hbox (badness 1009) in paragraph at lines 2428--2435
\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
[906]
Underfull \hbox (badness 7273) in paragraph at lines 2510--2514
[][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p
tm/m/n/10 and
[907] [908] [909] [910]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2758--2758
[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[911]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2795--2795
[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[912] [913]
Underfull \hbox (badness 1226) in paragraph at lines 2923--2927
\T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1
/pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy
[914]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2976--2976
[]\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 2980--2980
[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[915]
Underfull \hbox (badness 10000) in paragraph at lines 3042--3045
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1
/pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3093--3093
[]\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w
rong" message:[]
[916] [917] [918]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3257--3257
[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3262--3262
[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[919] [920]
Underfull \hbox (badness 10000) in paragraph at lines 3404--3409
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f
ied, raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3404--3409
[][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true,
the grid is reg-u-lar and ei-ther
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[][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt
m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is
[921] [922] [923]
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[924] [925] [926]
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[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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[] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l
engths & coords[]
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[] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
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[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc
r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[]
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[]\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow
(VADeaths)))[]
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[]\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7
, lty = 1:7,[]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
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[]\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset
= .02",inset = .02)[]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
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[]\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized"
, "columns."),[]
[929]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth
od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\
T1/pcr/m/n/10 type %in%
[930]
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[931] [932] [933]
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[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
[934]
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[]\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
[935] [936] [937] [938] [939]
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[]\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
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[]\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
[940] [941]
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor,[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
[942]
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\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/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 axis[][][][]\T1/ptm/m/n/10 ,
[943] [944] [945] [946]
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[947 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//mai.pdf>]
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[948 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//oma.pdf>]
[949] [950]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[952] [953] [954] [955] [956]
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[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
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[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
[957]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again>
\relax
l.5943 \aliasA{plot}{plot.default}{plot}
[958] [959] [960] [961] [962]
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[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[963] [964]
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[] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co
llapse = "\n")),[]
[965] [966] [967] [968]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[969] [970]
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[]\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
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[][]
[971 </usr/src/RPM/BUILD/R-4.2.2/library/graphics/help/figures//pch.pdf>]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
[972]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[974]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[975]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T
1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or
[976] [977] [978] [979]
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[980] [981] [982] [983] [984] [985]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
[986]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[987] [988] [989] [990] [991]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[992] [993] [994]
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[]\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)
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[]\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)[]
[995] [996]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
[997]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh
tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 )
is drawn. For
[998]
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[]
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
lambda = 2),[]
[999] [1000]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[1001] [1002]
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[] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile:
Règles, Liberté, Egalité, Fraternité...")[]
[1003]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m
/n/10 par(c("font.sub",
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[]\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 a
re []\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
[1004]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again>
\relax
l.9018 \HeaderA{units}{Graphical Units}{units}
[1005]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[1006] [1007]
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[]\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)[]
[1008]) (./grid-pkg.tex
Chapter 6.
[1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018]
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
to the
[1019] [1020] [1021] [1022] [1023] [1024]
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
[1025] [1026] [1027]
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[] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
[1028] [1029] [1030] [1031]
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[]\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
[1032] [1033] [1034] [1035] [1036] [1037] [1038]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[1039] [1040] [1041]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[]
[1042]
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[]\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 ,
[1043]
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[]\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
[1044] [1045] [1046]
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[]\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
[1047] [1048] [1049]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
[1050]
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
[1051] [1052]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
[1053]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[1054] [1055]
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[]\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix;
see
[1056] [1057] [1058]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[1059] [1060] [1061] [1062] [1063]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1064] [1065]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just=
c("left", "bottom")))[]
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[]\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa
ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see
[1066] [1067]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
[1068] [1069] [1070]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
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[]\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[]
[1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082]
[1083]
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[]\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
[1084] [1085] [1086] [1087]
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
[1088] [1089]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve
c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list
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\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For
[]\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther
[1096] [1097]
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[]\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob
-ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a
[1098] [1099] [1100]
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a
r-gu-ments above are passed to
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[1112] [1113] [1114] [1115] [1116] [1117]
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
[1118]
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[]\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip()
, device=TRUE)
[1119] [1120]
Underfull \hbox (badness 1867) in paragraph at lines 7122--7124
[]\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
[1121]
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[][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push
Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 ,
[1122] [1123] [1124] [1125] [1126]
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
[1127]) (./methods-pkg.tex [1128]
Chapter 7.
[1129] [1130]
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
co-erce meth-ods work. Use
[1131] [1132] [1133]
Underfull \hbox (badness 1348) in paragraph at lines 392--395
[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in-
for-ma-tion about group generic func-tions; [][]Meth-
[1134] [1135]
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[]\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall
y a primitive.[]
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[]\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[]
[1136]
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[]\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[]
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[]\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[]
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[]\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b
y callNextMethod[]
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[]\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
"B0" method[]
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[]\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[
]
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[1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
[1150] [1151] [1152]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
[1153] [1154]
Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
[]\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/
10 can be an ob-ject of class
[1155] [1156] [1157]
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[]\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 =
[1158] [1159]
Underfull \hbox (badness 10000) in paragraph at lines 2327--2331
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment
[][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
[1160] [1161] [1162]
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[]\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\
T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c
re-ate ob-jects of class
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[]\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
[1163]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1164] [1165] [1166]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1167] [1168] [1169] [1170] [1171] [1172] [1173]
Underfull \hbox (badness 10000) in paragraph at lines 3402--3407
[]\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r
e-turns the im-plicit generic ver-sion,
Underfull \hbox (badness 6268) in paragraph at lines 3402--3407
[]\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici
t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents
[1174] [1175]
Underfull \hbox (badness 10000) in paragraph at lines 3530--3534
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10
getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class
[1176]
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[]
[1177] [1178]
Underfull \hbox (badness 10000) in paragraph at lines 3761--3762
[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit
ude =
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
[1179]
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,
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[]\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
[1180] [1181] [1182] [1183] [1184] [1185]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312
[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
[1186]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1187] [1188] [1189]
Underfull \hbox (badness 2126) in paragraph at lines 4578--4586
[]\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 ,
[1190] [1191] [1192]
Underfull \hbox (badness 10000) in paragraph at lines 4815--4824
[]\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
[1193] [1194] [1195] [1196]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1197]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[1199]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1200] [1201]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1202] [1203] [1204]
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[]\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
[1205] [1206] [1207] [1208] [1209] [1210]
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p
tm/m/n/10 is equiv-a-lent to in-vok-ing the method
[1211] [1212]
Underfull \hbox (badness 1248) in paragraph at lines 6351--6355
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T
1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions,
Underfull \hbox (badness 1960) in paragraph at lines 6351--6355
\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
[1213]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1214] [1215]
Underfull \hbox (badness 2875) in paragraph at lines 6655--6664
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][][]\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
[1216]
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[1218] [1219]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6981 \aliasA{S4}{S3Part}{S4}
[1220]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
[1221] [1222]
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[]\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
datasets::iris)[]
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[]\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[]
[1223]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again>
\relax
l.7237 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
ignored
<to be read again>
\relax
l.7239 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again>
\relax
l.7240 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.7242 \aliasA{Ops}{S4groupGeneric}{Ops}
pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7243 \aliasA{Summary}{S4groupGeneric}{Summary}
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[]\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
[1224]
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[]\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p
tm/m/n/10 , []\T1/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 7317--7329
[]\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p
tm/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 "c
os"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp
i"[]\T1/ptm/m/n/10 ,
[1225] [1226]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
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[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS
uperClasses() []\T1/ptm/m/n/10 which calls
[1227]
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[]\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[]
[1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238]
[1239] [1240]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1241]
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1242] [1243] [1244] [1245]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1246] [1247] [1248]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1249] [1250] [1251]
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[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
[1252] [1253] [1254] [1255]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1256]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
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[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi
on" []\T1/ptm/m/n/10 for class
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[]\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.,
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[]\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10
"function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1267] [1268] [1269]) (./parallel-pkg.tex [1270]
Chapter 8.
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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p
cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][]
RNG[][][]: see
[1271]
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[]\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a
nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for
[1272] [1273]
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[]\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
[1274]
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD,
So-laris and Win-dows.
[1275] [1276]
Underfull \hbox (badness 10000) in paragraph at lines 445--447
[]\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
[1277] [1278] [1279] [1280] [1281]
Underfull \hbox (badness 1917) in paragraph at lines 779--788
[]\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 779--788
[]\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe
s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If
[1282] [1283]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 872--872
[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1284] [1285] [1286]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
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[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1287]
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[]\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
[1288]
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[]\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 1243--1243
[]\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)[]
[1289] [1290]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1359--1359
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
[1291]
Underfull \hbox (badness 1577) in paragraph at lines 1402--1405
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10
.Random.seed []\T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1449--1451
[]\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
[1292] [1293]) (./splines-pkg.tex [1294]
Chapter 9.
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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1303]
Underfull \hbox (badness 1043) in paragraph at lines 597--599
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec
t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the
[1304] [1305]
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[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1306] [1307] [1308]) (./stats-pkg.tex
Chapter 10.
[1309]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\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"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
[]\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
Species" with 3 levels:[]
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[] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
list, as no factors[]
[1310] [1311] [1312] [1313] [1314]
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[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
[1315]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
[1316] [1317] [1318] [1319] [1320] [1321]
Underfull \hbox (badness 1024) in paragraph at lines 887--889
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l
m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for
[1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1625--1625
[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
[1333] [1334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1775--1775
[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
[1335]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1787--1787
[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
]
[1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346]
[1347] [1348] [1349]
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[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1350] [1351] [1352] [1353]
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[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1354] [1355] [1356]
Underfull \hbox (badness 10000) in paragraph at lines 3264--3266
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo
geneity of
[1357]
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[]\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 3314--3314
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1358] [1359] [1360] [1361]
Package amsmath Warning: Foreign command \atopwithdelims;
(amsmath) \frac or \genfrac should be used instead
(amsmath) on input line 3642.
[1362]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3708--3708
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1363] [1364] [1365] [1366]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3987--3987
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1367] [1368] [1369] [1370] [1371]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4276--4276
[]\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 4277--4277
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1372] [1373] [1374] [1375]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4518--4518
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1376] [1377]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4693--4693
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1378] [1379]
Underfull \hbox (badness 3989) in paragraph at lines 4787--4794
[]\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 =
[1380] [1381] [1382] [1383] [1384]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5172--5172
[]\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))[]
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[]\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))[]
[1385] [1386] [1387]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5396--5396
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
[1388] [1389] [1390] [1391]
Underfull \hbox (badness 1436) in paragraph at lines 5624--5629
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
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\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 5624--5629
\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 ,
[1392] [1393] [1394]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5827--5827
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1395] [1396]
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[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1397] [1398] [1399]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6179--6179
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1400] [1401]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6287--6287
[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
[1402] [1403] [1404] [1405]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1406]
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[]\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca
n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing
method
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[]\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g
ram []\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 6639--6644
\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,
[1407]
Underfull \hbox (badness 7238) in paragraph at lines 6675--6678
[][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti
on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend
rogram[][][] []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[]
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[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
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[]\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):[]
[1408]
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[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
[1409] [1410] [1411]
Underfull \vbox (badness 10000) has occurred while \output is active [1412]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6994--6994
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1413] [1414]
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[1416] [1417] [1418]
Underfull \hbox (badness 10000) in paragraph at lines 7394--7398
[]\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 "bi
nary" []\T1/ptm/m/n/10 or
[1419]
Underfull \hbox (badness 6493) in paragraph at lines 7493--7496
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][]
\T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the
[1420] [1421]
Underfull \hbox (badness 10000) in paragraph at lines 7630--7633
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427]
Underfull \hbox (badness 10000) in paragraph at lines 8042--8047
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences []
\T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 ,
...,
[1428] [1429] [1430] [1431] [1432] [1433]
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[]\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al
so be sup-plied as named ar-gu-ments to
[1434] [1435] [1436] [1437] [1438] [1439]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8860--8860
[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
[1440]
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[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
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[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
[1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9488--9488
[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9489--9489
[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
[1449] [1450] [1451]
Underfull \hbox (badness 7291) in paragraph at lines 9668--9670
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test
of homogeneity of
[1452] [1453] [1454] [1455] [1456] [1457] [1458]
Underfull \hbox (badness 6944) in paragraph at lines 10160--10166
[][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in-
ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment
);
[1459] [1460] [1461]
Underfull \hbox (badness 3758) in paragraph at lines 10374--10377
[]\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
[1462] [1463] [1464] [1465]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10618--10618
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1466]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
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[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second
[]\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 10788--10791
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic
ients[][][][]\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
[1468] [1469] [1470]
Underfull \hbox (badness 2142) in paragraph at lines 11005--11008
[]\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 ^^@
[1471]
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[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1472]
Underfull \hbox (badness 10000) in paragraph at lines 11128--11134
[][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1
0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1
0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11166--11171
[]\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui
tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (=
[1473] [1474]
Underfull \hbox (badness 2635) in paragraph at lines 11299--11302
\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/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 )
meth-ods and the
[1475] [1476] [1477]
Underfull \hbox (badness 1694) in paragraph at lines 11482--11485
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1478]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11580--11580
[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
[1479]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11613--11613
[] \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 11626--11630
[]\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\
T1/ptm/m/n/10 (the de-fault) or
[1480] [1481] [1482] [1483] [1484]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11948--11948
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
[1485]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again>
\relax
l.11963 \aliasA{hat}{influence.measures}{hat}
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12023--12023
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
[1486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12035--12035
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
Underfull \hbox (badness 1062) in paragraph at lines 12088--12093
[]\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me
nts are there to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12105--12107
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists
mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1487] [1488] [1489] [1490]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12360--12360
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12361--12361
[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 10000) in paragraph at lines 12707--12709
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de
fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12730--12732
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 3417) in paragraph at lines 13037--13039
[]\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 []\T1/pcr/m/n/10 ob <-
Underfull \hbox (badness 2894) in paragraph at lines 13043--13047
[]\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 13043--13047
\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti
ve (or true), trac-ing in-for-ma-tion on the
[1502] [1503] [1504] [1505] [1506] [1507]
Underfull \hbox (badness 1496) in paragraph at lines 13457--13463
[]\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran-
dom-iza-tion Dis-tri-bu-tions of
[1508] [1509] [1510] [1511]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13706--13706
[]\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[]
[1512]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13807--13807
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1513]
Underfull \hbox (badness 4518) in paragraph at lines 13855--13860
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516]
Underfull \hbox (badness 10000) in paragraph at lines 14062--14066
[]\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava
il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][]
[]\T1/ptm/m/n/10 ,
[1517] [1518] [1519] [1520] [1521]
Underfull \hbox (badness 1163) in paragraph at lines 14402--14410
\T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc
on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re
siduals[][][][]\T1/ptm/m/n/10 ,
[1522] [1523]
Underfull \hbox (badness 4518) in paragraph at lines 14522--14527
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1524] [1525] [1526]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14710--14710
[]\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 14711--14711
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1527] [1528] [1529] [1530] [1531]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15054--15054
[]\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 15055--15055
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1532]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 15148--15148
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1533] [1534] [1535] [1536] [1537] [1538] [1539]
Underfull \hbox (badness 2726) in paragraph at lines 15557--15560
[]\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [
]\T1/pcr/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 ,
[1540]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15651--15651
[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
[1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 16278--16278
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1551] [1552]
Underfull \hbox (badness 1490) in paragraph at lines 16425--16430
\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
[1553]
Underfull \hbox (badness 1648) in paragraph at lines 16491--16493
[]\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,
[1554]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16576--16576
[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16577--16577
[]\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[]
[1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17134--17134
[]\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[]
[1564] [1565] [1566]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17366--17366
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576]
Underfull \vbox (badness 10000) has occurred while \output is active [1577]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 18088--18088
[]\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
Underfull \vbox (badness 10000) has occurred while \output is active [1578]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 18106--18106
[]\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n
umerical differentiation,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 18107--18107
[]\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo
w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 18111--18111
[]\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co
nverging on *some*):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18112--18112
[]\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal
ler than above[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 18115--18115
[] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl
("^NixOS", osVersion)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18147--18147
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1579] [1580] [1581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18323--18323
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
[1582]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18370--18370
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18417--18417
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1583] [1584] [1585] [1586]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 18623--18623
[] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[]
[1587] [1588] [1589] [1590] [1591]
Underfull \hbox (badness 1248) in paragraph at lines 18938--18941
[]\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 1661) in paragraph at lines 18951--18955
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18959--18963
\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
[1592]
Underfull \hbox (badness 2042) in paragraph at lines 19017--19019
[]\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
[1593]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 19123--19123
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
[1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19166--19166
[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19184--19184
[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19187--19187
[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19207--19207
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
[1595]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19210--19210
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
Underfull \hbox (badness 2564) in paragraph at lines 19245--19256
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva
l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m
/n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/
10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19245--19256
\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
[1596]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19308--19308
[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1597] [1598] [1599]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19535--19535
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1600] [1601]
Underfull \hbox (badness 1337) in paragraph at lines 19646--19649
[]\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
[1602] [1603] [1604] [1605] [1606]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19965--19965
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1607] [1608]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 20053--20053
[] \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 (12.78088pt too wide) in paragraph at lines 20055--20055
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20057--20057
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1609]
Underfull \hbox (badness 10000) in paragraph at lines 20117--20123
\T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di
stance", lty = cook.lty,
Underfull \hbox (badness 10000) in paragraph at lines 20117--20123
\T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp
Underfull \hbox (badness 10000) in paragraph at lines 20125--20131
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T
1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 20136--20139
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m
/n/10 ylim <-
[1610] [1611] [1612] [1613] [1614]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20437--20437
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 1194) in paragraph at lines 20447--20450
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1615]
Underfull \hbox (badness 1107) in paragraph at lines 20505--20507
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate []
\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to
[1616]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20560--20560
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20567--20567
[]\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)[]
[1617] [1618]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20661--20661
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1619] [1620]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20790--20790
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1621]
Underfull \hbox (badness 7740) in paragraph at lines 20853--20855
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [
]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20901--20901
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1622]
Underfull \hbox (badness 10000) in paragraph at lines 20957--20959
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 polym(*, coefs=<non-NULL>)[]\T1/ptm/m/n/10 , and
[1623]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20994--20994
[] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or
just poly():[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20999--20999
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634]
[1635] [1636]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 21854--21854
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[]
[1637]
Underfull \hbox (badness 6859) in paragraph at lines 21921--21928
[][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21932--21938
[]\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/1
0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 ,
[1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648]
[1649]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22678--22678
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1650] [1651] [1652] [1653] [1654]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22962--22962
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22963--22963
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1655] [1656] [1657] [1658] [1659]
Underfull \hbox (badness 1337) in paragraph at lines 23289--23295
[]\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
[1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667]
Underfull \hbox (badness 10000) in paragraph at lines 23848--23850
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 23848--23850
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 23855--23856
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
[1668] [1669]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 23966--23966
[] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[]
[1670]
Underfull \hbox (badness 1028) in paragraph at lines 24024--24027
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T
1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and
[1671] [1672]
Underfull \hbox (badness 10000) in paragraph at lines 24139--24142
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\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 [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1673]
Underfull \hbox (badness 7099) in paragraph at lines 24258--24260
[]\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 [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1674]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24293--24293
[]\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median,
decreasing=TRUE))[]
[1675]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24369--24369
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1676] [1677]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24486--24486
[]\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with
care)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24487--24487
[]\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long
format[]
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[]\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time
variable[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24489--24489
[]\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v
ariable[]
[1678] [1679]
Underfull \hbox (badness 10000) in paragraph at lines 24649--24654
[][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[]
[][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r
e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [
][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 24649--24654
[][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing
con-tin-gency ta-bles and con-vert-ing them back to
[1680]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24660--24660
[]\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24661--24661
[]\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24680--24680
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1681]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24784--24784
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
[1682]
Underfull \hbox (badness 1033) in paragraph at lines 24827--24833
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
Underfull \hbox (badness 10000) in paragraph at lines 24848--24851
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r
unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] =
[1683]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24930--24930
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1684]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24959--24959
[]\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
used to fail badly (notably for "Turlach"):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24971--24971
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
[1685] [1686] [1687] [1688] [1689] [1690] [1691]
Underfull \hbox (badness 6268) in paragraph at lines 25429--25434
[][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S
Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo
mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 ,
[1692] [1693] [1694] [1695]
Underfull \hbox (badness 1867) in paragraph at lines 25638--25640
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods.
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 25653--25657
[]\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba
ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25653--25657
\T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where
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 25689--25689
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25696--25696
[]\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[]
[1696] [1697] [1698]
Underfull \hbox (badness 2495) in paragraph at lines 25879--25888
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1699] [1700]
Underfull \hbox (badness 2197) in paragraph at lines 26021--26024
[]\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion,
[]\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and
[1701]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 26041--26041
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
Underfull \hbox (badness 1412) in paragraph at lines 26048--26050
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1702]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26135--26135
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 26160--26160
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 26163--26163
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1703] [1704] [1705]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26392--26392
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 26396--26402
[]\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/
10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in
g only
[1706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26442--26442
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26463--26463
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1707] [1708] [1709]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26655--26655
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1710] [1711] [1712] [1713] [1714] [1715] [1716]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 27035--27035
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1717] [1718]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27216--27216
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 27222--27222
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))
for when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27231--27231
[]\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 27232--27232
[]\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 [1719]
Underfull \hbox (badness 2922) in paragraph at lines 27301--27306
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1720]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27338--27338
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27341--27341
[] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27350--27350
[] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27351--27351
[] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
# (Asym + R0)/2[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27355--27355
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1721]
Underfull \hbox (badness 3240) in paragraph at lines 27409--27412
[][][]\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 graph show-ing the []\T1/pcr/m/n/10 SSasympOff
[1722]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27430--27430
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27433--27433
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1723]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27516--27516
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27520--27520
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 27530--27530
[] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2),
phi[1]), pos=0, las=1)[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 27535--27535
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
[1724]
Underfull \hbox (badness 2922) in paragraph at lines 27571--27577
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27593--27593
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
[1725]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27609--27609
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 27623--27623
[]\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af
ter increasing maxiter !}[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27625--27625
[] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[]
Overfull \hbox (128.58029pt too wide) in paragraph at lines 27628--27628
[]\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, control = list(scaleOffset=1))[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 27630--27630
[] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1
e-11, nDcentral=TRUE), trace=TRUE)[]
[1726] [1727]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 27742--27742
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1728]
Underfull \hbox (badness 2922) in paragraph at lines 27804--27809
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27842--27842
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1729]
Underfull \hbox (badness 2922) in paragraph at lines 27891--27896
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1730]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27922--27922
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
Underfull \hbox (badness 2922) in paragraph at lines 27956--27961
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1731]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27981--27981
[]\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number
of iter...: 0" :[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27985--27985
[]\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28005--28005
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28015--28015
[] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x =
xmid = 2) = 2.5[]
[1732]
Underfull \hbox (badness 2922) in paragraph at lines 28050--28055
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28072--28072
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1733]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28090--28090
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
Underfull \hbox (badness 6493) in paragraph at lines 28142--28147
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1734]
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[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
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[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
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[]\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[]
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[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
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[]\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
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
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[]\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
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
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[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
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[]\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[]
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[]\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
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[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
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[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
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[]\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was
given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\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:[]
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[]\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
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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[]\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno
t compute exact p-value with ties[]
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[]\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9)
# same ties as (4:2, 3:1)[]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
= getOption("ts.eps"), ...)[]
[1801]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
[1802] [1803]
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[]\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 "")[]
[1804]) (./stats4-pkg.tex
Chapter 11.
[1805] [1806] [1807]
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
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[]\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos
er to 0 and 1[]
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(./tcltk-pkg.tex [1816]
Chapter 12.
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[]
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[]\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i
ng any Tk or Tcl com-mand by sim-ply run-ning
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[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
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[][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep
t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/
n/10 (whose
[1836]) (./tools-pkg.tex
Chapter 13.
[1837]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1838]
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[]\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1840]
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[]\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
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n
/10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n
/10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE,
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin
e to use. Over-rides any
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
ub-di-rec-tory
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[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
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[] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[]
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[]\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[]
[1854]
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[]\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
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a
pre-vi-ous
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\
T1/ptm/m/n/10 and
[1855]
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[]\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in-
her-it-ing from class
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[]\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [
]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1
/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with
char-ac-ter columns con-tain-ing most
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu
r-rent pack-ages in the CRAN pack-age repos-i-
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\T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta
iner in-for-ma-tion not pro-vided by
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[]\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR
AN_current_db []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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[]\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests",
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor,
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the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ig
nored
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[1869]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio
n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the
pack-age
[1870]
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[] \T1/pcr/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option
s: width=100 alt="R logo"}})",[]
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[]\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-
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\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-
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\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
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\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
[1872]
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[]\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str
ong",
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
sub-set of
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[]\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests",
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor,
[1873]
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[]\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[]
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[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
= TRUE)[]
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[]
[1878]
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[]\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
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[]\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal =
FALSE)
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[]\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal =
FALSE)[]
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-
tor of links, as re-turned by
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
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[]\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10
, \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10
,
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[]\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
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[]
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[]\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if
in-stalled. This should be run with
[1896] [1897]
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[]\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5
.0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti
on
[1898] [1899] [1900] [1901]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4276--4276
[] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[]
[1902] [1903]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 4438--4438
[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts =
"", copyright, bugs)
Underfull \hbox (badness 3118) in paragraph at lines 4449--4453
[]\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m
sgmerge []\T1/ptm/m/n/10 in ad-di-tion to
Underfull \hbox (badness 10000) in paragraph at lines 4453--4456
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig
ht[]\T1/ptm/m/n/10 ' and
[1904]
Underfull \hbox (badness 6859) in paragraph at lines 4469--4474
[]\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/ptm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 4477--4483
[]\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 4477--4483
\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
[1905] [1906] [1907]
Underfull \hbox (badness 10000) in paragraph at lines 4703--4705
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10
, such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or
[1908]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733
[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[]
Underfull \hbox (badness 3240) in paragraph at lines 4746--4749
[]\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 ',
Underfull \hbox (badness 1742) in paragraph at lines 4750--4760
[]\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe
nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4788--4794
[]\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo
r R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4788--4794
\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 ',
[1909]
Underfull \hbox (badness 1571) in paragraph at lines 4816--4820
[]\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
Underfull \hbox (badness 2772) in paragraph at lines 4842--4847
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][
]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat
-ing ex-ist-ing
[1910] [1911]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4984--4984
[]\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[]
[1912]) (./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 `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
[1913] [1914] [1915] [1916]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 258--258
[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1917]
Underfull \hbox (badness 10000) in paragraph at lines 378--383
\T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min
imize",
[1918]
Underfull \hbox (badness 10000) in paragraph at lines 384--386
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow
han-dles, by de-fault pro-duced by
[1919]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450
[]\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F
irefox window[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 452--452
[]\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
"Firefox"))[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469
[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1920] [1921] [1922]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683
[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
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[]\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 690--690
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691
[]\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 692--692
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Underfull \hbox (badness 10000) in paragraph at lines 726--732
[]\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 726--732
[]\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a
spell_package_C_files []\T1/ptm/m/n/10 per-form spell check-
[1923] [1924] [1925] [1926] [1927]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1049--1049
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1928]
Underfull \hbox (badness 1748) in paragraph at lines 1115--1123
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/pcr/m/n/
10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$
\T1/ptm/m/n/10 , in-di-cat-
Underfull \hbox (badness 2961) in paragraph at lines 1115--1123
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
Underfull \hbox (badness 1092) in paragraph at lines 1115--1123
\T1/ptm/m/n/10 as [][][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max", 1
) []\T1/ptm/m/n/10 which is []\T1/pcr/m/n/10 1 []\T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1115--1123
\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 1127--1129
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1929]
Underfull \hbox (badness 10000) in paragraph at lines 1235--1238
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1930] [1931]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1318--1318
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1932] [1933] [1934] [1935] [1936]
Underfull \hbox (badness 1859) in paragraph at lines 1721--1730
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
Underfull \hbox (badness 2042) in paragraph at lines 1721--1730
\T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1
/ptm/m/n/10 never re-turns. Do not re-port that
[1937] [1938]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1826--1826
[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[1939]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1861--1861
[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1940]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2007--2007
[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1941]
Underfull \hbox (badness 2277) in paragraph at lines 2076--2081
[]\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p
tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes
[1942]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2109--2109
[]\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct",
"upper", "xdigit")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2111--2111
[]\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2119--2119
[]\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
Unicode 13.)[]
[1943] [1944] [1945]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2267--2267
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1946]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2319--2319
[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1947] [1948]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2489--2489
[] \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")[]
[1949]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2512--2512
[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[1950]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2632--2632
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1951]
Underfull \hbox (badness 1082) in paragraph at lines 2706--2710
[][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab
out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file
s;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2711 ... the Clipboard in MS Windows}{clipboard}
[1952]
Underfull \hbox (badness 1163) in paragraph at lines 2742--2744
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1953]
Underfull \hbox (badness 10000) in paragraph at lines 2835--2837
[]\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
[1954] [1955] [1956] [1957]
Underfull \hbox (badness 10000) in paragraph at lines 3053--3055
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1958] [1959] [1960] [1961]
Underfull \hbox (badness 1762) in paragraph at lines 3346--3349
[]\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 []\T1/pcr/m/n/10 package =
[1962]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3438--3438
[]\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se
ts in the rpart package[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3439--3439
[]\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 '[]
[1963]
Underfull \hbox (badness 2452) in paragraph at lines 3515--3518
[]\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
[1964] [1965] [1966] [1967] [1968] [1969]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3931--3931
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[1970]
Underfull \hbox (badness 4779) in paragraph at lines 4010--4015
[]\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10
was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use
[1971]
Underfull \hbox (badness 1072) in paragraph at lines 4073--4077
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the
[1972]
Underfull \hbox (badness 7238) in paragraph at lines 4129--4134
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1
0 via \T1/ptm/m/n/10 the en-vi-ron-
Underfull \hbox (badness 1337) in paragraph at lines 4129--4134
\T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or
[]\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : /
/ curl . se / libcurl / c /
Underfull \hbox (badness 1184) in paragraph at lines 4144--4160
\T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10
'. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-
[1973]
Underfull \hbox (badness 4660) in paragraph at lines 4261--4264
\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
[1974]
Underfull \hbox (badness 10000) in paragraph at lines 4285--4287
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do
wnload.file[][][] []\T1/ptm/m/n/10 and
[1975] [1976]
Underfull \hbox (badness 1565) in paragraph at lines 4470--4474
[]\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
[1977]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4553--4553
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[1978]
Underfull \hbox (badness 1910) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p
le is run and
Underfull \hbox (badness 1655) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [
]\T1/ptm/m/n/10 sets the same state as
Underfull \hbox (badness 2846) in paragraph at lines 4587--4594
[]\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac
k-age's ex-am-ples. This is cur-
Underfull \hbox (badness 3460) in paragraph at lines 4587--4594
\T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau
lt", "default",
Underfull \hbox (badness 1931) in paragraph at lines 4594--4601
[]\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di
-cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1979] [1980] [1981] [1982]
Underfull \hbox (badness 5939) in paragraph at lines 4840--4842
[]\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n
/10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault
[1983] [1984]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4983--4983
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1985]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.5054 ...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
<to be read again>
\relax
l.5054 ...mat Unordered and Ordered Lists}{format}
[1986] [1987] [1988]
[1989] [1990] [1991] [1992] [1993]
Underfull \hbox (badness 1622) in paragraph at lines 5577--5581
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
to ex-ter-nal GUIs or to the
[1994] [1995] [1996] [1997] [1998] [1999]
Underfull \hbox (badness 1448) in paragraph at lines 5956--5961
[]\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject
s, cor-re-spond-ing to call-ing
[2000] [2001]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 6106--6106
[]\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 6118--6118
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
[2002] [2003]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6251--6251
[] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 6252--6252
[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
[2004] [2005] [2006]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6462--6462
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[2007]
Underfull \hbox (badness 10000) in paragraph at lines 6546--6548
[]\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
[2008]
Underfull \hbox (badness 1502) in paragraph at lines 6595--6600
[]\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 6595--6600
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[2009] [2010]
Underfull \hbox (badness 10000) in paragraph at lines 6768--6777
[]\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 6768--6777
\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
[2011]
Underfull \hbox (badness 2150) in paragraph at lines 6832--6835
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
[2012]
Underfull \hbox (badness 5175) in paragraph at lines 6848--6851
[]\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc
h database for sub-se-quent use by
[2013]
Underfull \hbox (badness 3118) in paragraph at lines 6971--6973
[]\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
[2014] [2015] [2016]
Underfull \hbox (badness 5091) in paragraph at lines 7146--7148
[]\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 10000) in paragraph at lines 7176--7183
[]\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends
", "Imports", "LinkingTo",
Underfull \hbox (badness 10000) in paragraph at lines 7176--7183
\T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports",
Underfull \hbox (badness 1270) in paragraph at lines 7176--7183
\T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in
-stalls all the pack-ages
Underfull \hbox (badness 1270) in paragraph at lines 7191--7201
\T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla
g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If
[2017]
Underfull \hbox (badness 4441) in paragraph at lines 7234--7237
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed to
Underfull \hbox (badness 2837) in paragraph at lines 7234--7237
[]\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall.
E.g., []\T1/pcr/m/n/10 c("--html",
Underfull \hbox (badness 1424) in paragraph at lines 7242--7245
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
[2018]
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n
/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7313--7320
\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 7313--7320
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
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[]\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt
m/m/n/10 al-ways works pro-vided the pack-age con-tains no
[2019]
Underfull \hbox (badness 1314) in paragraph at lines 7401--7408
[]\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute
all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 7481--7486
[][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac
kages[][][][]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
[2021]
Underfull \hbox (badness 5133) in paragraph at lines 7540--7544
[]\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 7554--7557
[]\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10
DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7601--7601
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[2022] [2023]
Underfull \hbox (badness 4132) in paragraph at lines 7725--7727
[]\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
[2024] [2025] [2026]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7892--7892
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[2027] [2028] [2029]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8035--8035
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
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[]\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
[2030] [2031]
Underfull \hbox (badness 10000) in paragraph at lines 8180--8182
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
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[]\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 S3 class
[2032] [2033] [2034] [2035]
Underfull \hbox (badness 1859) in paragraph at lines 8413--8416
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
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\T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/
n/10 el-e-ments with names start-ing with a suit-able pre-fix
[2036]
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[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d
b"[]\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 8518--8518
[]\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8526--8526
[]\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):[]
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[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[2037] [2038]
Underfull \hbox (badness 1917) in paragraph at lines 8621--8623
[]\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/
n/10 ,
[2039] [2040] [2041] [2042]
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[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8894--8894
[] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8895--8895
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[2043]
Underfull \hbox (badness 10000) in paragraph at lines 8923--8925
[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\
T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 8937--8939
[]\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut
, al-low-ing things like []\T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8945--8950
[]\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,
[2044]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8991--8991
[] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[]
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[] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[]
[2045] [2046]
Underfull \hbox (badness 10000) in paragraph at lines 9121--9126
[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade",
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[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("installed", "not
[2047]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
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[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[2048] [2049] [2050]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9418--9418
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[2051]
Underfull \hbox (badness 1789) in paragraph at lines 9551--9553
[]\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
[2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060]
Underfull \hbox (badness 5203) in paragraph at lines 10124--10127
[]\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
[2061] [2062] [2063]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10374--10374
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[2064] [2065]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10535--10535
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[2066] [2067] [2068]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10716--10716
[]\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[]
[2069]
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
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[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2070]
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[]\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force
s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL
[2071] [2072] [2073] [2074]
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[]\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC",
"HPD"),
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[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 11169--11174
\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER
S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2075] [2076] [2077] [2078]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11402--11402
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2079] [2080] [2081] [2082]
Underfull \hbox (badness 10000) in paragraph at lines 11663--11667
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[]
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[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[2083] [2084]
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[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
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[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
[2085] [2086]
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[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[2087] [2088]
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[]\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n
ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me
nt vari-
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\T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10
. If this is set, then it takes prece-dence over
Overfull \hbox (106.98032pt too wide) in paragraph at lines 12110--12110
[]\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 '[]
[2089]
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[] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news",
"Rfunctions",[]
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[] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig
nettes"),[]
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[] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s
ubject",[]
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[] \T1/pcr/m/n/10 "subject:descending", "size", "size:de
scending"),[]
[2090]
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\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,
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\T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re
-verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12274--12274
[]\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes","
Rfunctions"))[]
[2091]
Underfull \hbox (badness 1377) in paragraph at lines 12330--12333
[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/
m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style
[2092]
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[][][]$\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 /
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12403--12403
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[2093] [2094] [2095]
Underfull \hbox (badness 10000) in paragraph at lines 12585--12589
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i
s now taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12618--12624
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][]
[]\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m
/n/10 out-put in
[2096] [2097]
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[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[2098]
Underfull \hbox (badness 1009) in paragraph at lines 12812--12824
[]\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
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[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows
and
[2099]
Underfull \hbox (badness 1043) in paragraph at lines 12895--12900
[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
con-fig-ured the map-ping of font num-bers to fonts, and
[2100] [2101] [2102] [2103]
Underfull \hbox (badness 1888) in paragraph at lines 13188--13191
[]\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-der. Where
Underfull \hbox (badness 10000) in paragraph at lines 13205--13208
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2104]
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[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
[2105]
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[]\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
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[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
[2106] [2107] [2108]
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2109]
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[]\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir
ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2110] [2111] [2112]
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[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
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[]\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
[][][]\T1/pcr/m/n/10 deparse[][][](control = <S>) []\T1/ptm/m/n/10 will not ha
ve
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha
s only a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic
h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it
y rea-sons;
[2113]
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[]\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau
lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to
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[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2114]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
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[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
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[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[2115] [2116] [2117]
Underfull \hbox (badness 10000) in paragraph at lines 14094--14096
[]\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
[2118]
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[]\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se
e
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[][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/
m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu-
[2119]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau
lt) then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt
m/m/n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 14252--14259
\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$"[]\T1/ptm/m/n/10 ) and
[2120] [2121]
Underfull \hbox (badness 2020) in paragraph at lines 14417--14425
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/
n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on
some plat-forms),
Underfull \hbox (badness 1194) in paragraph at lines 14417--14425
\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --
exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n
/10 ' (and sim-i-lar) and on Win-dows
[2122]
Underfull \hbox (badness 1622) in paragraph at lines 14426--14433
[]\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p
cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able
[2123]
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[]\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t
o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment
vari-able
Underfull \hbox (badness 10000) in paragraph at lines 14574--14577
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 14574--14577
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
[2124] [2125] [2126]
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[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
[2127] [2128] [2129] [2130] [2131] [2132]
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Underfull \hbox (badness 4467) in paragraph at lines 15208--15210
[]\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 15223--15227
\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
[2133]
Underfull \hbox (badness 1694) in paragraph at lines 15237--15241
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins
talled.packages[][][](lib.loc =
Underfull \hbox (badness 10000) in paragraph at lines 15243--15248
[]\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 15243--15248
\T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15243--15248
[]\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac
he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
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[]\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n
/10 available.packages(contriburl =
Underfull \hbox (badness 1226) in paragraph at lines 15279--15284
\T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa
ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
Underfull \hbox (badness 10000) in paragraph at lines 15300--15305
[]\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
[2134]
Underfull \hbox (badness 10000) in paragraph at lines 15308--15311
[][][]\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.pa
ckages[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15362--15362
[]\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt")
[2135] [2136] [2137]
Underfull \hbox (badness 2293) in paragraph at lines 15569--15572
[][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v
i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,
[2138]
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[]\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:[]
[2139]
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[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
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[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
[2140] [2141]
Underfull \hbox (badness 1297) in paragraph at lines 15805--15807
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2142]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil
l delete a menu and all of its items and sub-menus.
[2143] [2144]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2145]
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[]\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : []
\T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n
/10 and
Underfull \hbox (badness 10000) in paragraph at lines 16069--16071
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. []\T1/pcr/m/n/10 file =
[2146] [2147] [2148]) [2149] [2150] (./KernSmooth-pkg.tex
Chapter 15.
[2151]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2152] [2153] [2154] [2155] [2156]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2157] [2158] [2159] [2160]) (./MASS-pkg.tex
Chapter 16.
[2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182]
[2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193]
[2194]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2418--2418
[]\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 2422--2422
[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
[2195] [2196] [2197] [2198]
Underfull \hbox (badness 6559) in paragraph at lines 2701--2704
[]\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
[2199] [2200] [2201]
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[]\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo
gnormal"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2871--2876
[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi
al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
/10 "Poisson"[]\T1/ptm/m/n/10 ,
[2202] [2203]
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[]\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
[2204] [2205] [2206]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3234--3234
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
[2207]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv
et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and
[2220] [2221] [2222] [2223] [2224] [2225] [2226]
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",
...)[]
[2227] [2228] [2229]
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,
[2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]
[2241] [2242] [2243]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5930--5930
[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2244]
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[]\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")
[2245] [2246]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6151 ...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
<to be read again>
\relax
l.6151 ...sical N, P, K Factorial Experiment}{npk}
[2247] [2248] [2249]
[2250] [2251] [2252]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6571--6571
[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
[2253]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2254] [2255] [2256] [2257] [2258] [2259]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7098--7098
[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
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[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
[2260]
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[]\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 ) =
[2261]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2262] [2263]
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[]\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than
[]\T1/pcr/m/n/10 min(p,
[2264] [2265]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2266]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2267] [2268] [2269] [2270] [2271] [2272]
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[]\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
[2273] [2274]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8124--8124
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\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
[2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285]
[2286] [2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9529--9529
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2295]
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[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\
T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n
/10 ,
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[]\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-l
arly),
[2296]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9738--9738
[]\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 9740--9740
[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9743--9743
[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2297] [2298] [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] [2307]
[2308] [2309]) (./Matrix-pkg.tex [2310]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 35--38
[]\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
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2311]
Underfull \hbox (badness 1769) in paragraph at lines 89--92
[]\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
[2312]
Underfull \hbox (badness 2229) in paragraph at lines 153--156
[]\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 153--156
\T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor
, these ar-gu-ments will be con-cate-nated to a new
[2313]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 262--264
[]\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
[2314] [2315]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 445--445
[] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym
metry property[]
[2316]
Underfull \hbox (badness 5119) in paragraph at lines 488--492
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Overfull \hbox (4.38043pt too wide) in paragraph at lines 522--522
[]\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 524--524
[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
[2317]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 533--533
[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2318]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 647--647
[]\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:[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>) 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 '[]
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[]\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}"}.[]
[2319]
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[] \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?[]
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[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
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[]\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[]
[2320]
Underfull \hbox (badness 1874) in paragraph at lines 737--740
[]\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 https : / / netlib . org /
[2321] [2322]
Underfull \hbox (badness 1107) in paragraph at lines 860--865
\T1/ptm/m/n/10 sity'' of []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/
10 y[]\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n/10 code in []
\T1/pcr/m/n/10 selectMethod(cbind2,
Underfull \hbox (badness 10000) in paragraph at lines 903--908
[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/
10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met
h-ods:
[2323]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 967--967
[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2324]
Underfull \hbox (badness 3612) in paragraph at lines 1054--1057
[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "pMatrix") []\T1/ptm/m/n/10
re-turns the per-mu-ta-tion
[2325]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again>
\relax
l.1154 ...- '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
<to be read again>
\relax
l.1154 ...- 'Matrix' S4 Generic and Methods}{chol}
[2326] [2327]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2328]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1396--1396
[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
[2329]
Underfull \hbox (badness 2277) in paragraph at lines 1424--1427
[]\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
[2330]
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[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
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[]\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(<UTF-8>) gives bad plots[]
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[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529
[]\T1/pcr/m/n/9 str(re <- lapply(rr, expand), max.level=2) ## each has a \TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 matrix[]
[2331]
Underfull \hbox (badness 10000) in paragraph at lines 1565--1572
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("Cholesky", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 4673) in paragraph at lines 1565--1572
[]\T1/pcr/m/n/10 new("BunchKaufman", ...)[]\T1/ptm/m/n/10 , etc, or rather by c
alls of the form [][][]\T1/pcr/m/n/10 chol[][][](pm) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1600--1604
[]\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
[2332]
Underfull \hbox (badness 1221) in paragraph at lines 1616--1622
\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 .
Hence, for com-pat-i-bil-ity, the []\T1/pcr/m/n/10 "Cholesky" []\T1/ptm/m/n/10
and
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
has been already used, duplicate ignored
<to be read again>
\relax
l.1657 ... 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
<to be read again>
\relax
l.1657 ... 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
<to be read again>
\relax
l.1658 \aliasA{colMeans}{colSums}{colMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again>
\relax
l.1681 \aliasA{rowMeans}{colSums}{rowMeans}
pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again>
\relax
l.1694 \aliasA{rowSums}{colSums}{rowSums}
[2333pdfTeX warning (ext4): destinati
on with the same identifier (name{Rfn.rowMeans,diagonalMatrix.Rdash.method}) ha
s been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.1733 ## S4 method for signature 'CsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.rowSums,diagonalMatrix.Rdash.method}) h
as been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.1733 ## S4 method for signature 'CsparseMatrix'
]
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[]\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 1750--1754
\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 fr
om a
Underfull \hbox (badness 1237) in paragraph at lines 1761--1764
[][][]\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/1
0 , since
[2334] [2335]
Underfull \hbox (badness 3547) in paragraph at lines 1915--1918
[]\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
[2336] [2337] [2338] [2339] [2340] [2341]
Underfull \hbox (badness 7379) in paragraph at lines 2445--2447
[]\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
[2342] [2343] [2344]
Underfull \hbox (badness 10000) in paragraph at lines 2696--2699
[]\T1/pcr/m/n/10 signature(from = "dgTMatrix", to = "matrix")[]\T1/ptm/m/n/10 ,
and typ-i-cally co-er-cion
Underfull \hbox (badness 4846) in paragraph at lines 2721--2725
[]\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and []
[][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr
/m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 2726--2730
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
more than one pos-si-ble
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[]\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 a
nd [][][]\T1/pcr/m/n/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 ;
[2345]
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[] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE,
kind)[]
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[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
If miss-ing,
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[]\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
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[][][]\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
[2346]
Underfull \hbox (badness 1097) in paragraph at lines 2816--2819
[]\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 ldiMat
rix[][][] []\T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2829--2834
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][] []\T1/ptm/m/n/10 (the re-sult-ing clas
s de-pend-ing on []\T1/pcr/m/n/10 shape []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 k
ind[]\T1/ptm/m/n/10 ) rep-re-sen-ta-tion of
[2347]
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[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a []
[][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma
trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 6542) in paragraph at lines 2960--2964
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr
oup meth-ods re-turn a
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10
: the re-sult is from class
[2348pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coer
ce,diagonalMatrix,nMatrix.Rdash.method}) has been already used, duplicate ignor
ed
<argument> ...shipout:D \box_use:N \l_shipout_box
l.2975
]
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[]\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j
ect of S3 class
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[][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes
e 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
[2349] [2350]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 :
this group con-tains
[2351] [2352]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe
rent from the random one[]
[2353]
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[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][]
[]\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/
ptm/m/n/10 , via
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[]\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as
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[][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10
for ef-fi-ciency rea-sons only check the di-
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\T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p
tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion
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\T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][
][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see
[]\T1/pcr/m/n/10 selectMethod("coerce",
[2354] [2355]
Underfull \hbox (badness 10000) in paragraph at lines 3599--3603
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsCMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 2103) in paragraph at lines 3599--3603
[]\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v
ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 ,
[2356]
Underfull \hbox (badness 1571) in paragraph at lines 3649--3652
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10
: Re-turns (and stores) the
[2357] [2358]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3818
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class []
\T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse
Matrix"[]\T1/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3813--3818
\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 "compMatri
x" []\T1/ptm/m/n/10 by class
Underfull \hbox (badness 1400) in paragraph at lines 3825--3828
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10
: if []\T1/pcr/m/n/10 uplo ==
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 3896--3898
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsyMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1365) in paragraph at lines 3938--3941
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10
, or []\T1/pcr/m/n/10 x = "dsyMatrix"
[2360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3983--3983
[]\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ
internally :[]
[2361]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4116--4116
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
[2362]
Underfull \hbox (badness 3635) in paragraph at lines 4179--4183
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla
ss
Underfull \hbox (badness 10000) in paragraph at lines 4188--4191
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
[2363]
Underfull \hbox (badness 10000) in paragraph at lines 4193--4197
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n
/10 : the
[2364] [2365pdfTeX warning (ext4): destination with the same identifier (name{R
fn.coerce,dtrMatrix,dgeMatrix.Rdash.method}) has been already used, duplicate i
gnored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.4347 \item[\code{diag}:]
Object of class \code{"character"}. Must be]
Underfull \hbox (badness 2065) in paragraph at lines 4378--4382
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix", b = "....")[]\T1/ptm/m/n/10 efficie
ntely use a ``for-ward-solve'' or
[2366] [2367] [2368] [2369]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 4635--4635
[]\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe
ll-Boeing/counterx/counterx.html[]
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[] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB
/Boeing/msc00726.tar.gz"))))[]
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[]\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary
dir./folder:[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4649--4649
[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
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[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2370] [2371] [2372] [2373]
Underfull \hbox (badness 10000) in paragraph at lines 4937--4942
[]\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10
, and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][
][][]\T1/ptm/m/n/10 ,
[2374]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5018--5018
[]\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 5020--5020
[] \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 5024--5024
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2375]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5031--5031
[] \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 '[]
[2376] [2377]
Underfull \hbox (badness 4120) in paragraph at lines 5170--5173
[]\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
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5188--5188
[]\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) #
failed for 2 days ..[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5208--5208
[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5214--5214
[] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,
border.col=NA)[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5215--5215
[] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[]
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5219--5219
[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
[2378]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227
[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2379]
Underfull \hbox (badness 1817) in paragraph at lines 5326--5335
[]\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 wit
hin the
Underfull \hbox (badness 10000) in paragraph at lines 5368--5370
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
Underfull \hbox (badness 7081) in paragraph at lines 5370--5373
[]\T1/pcr/m/n/10 signature(from = "integer", to = "indMatrix")[]\T1/ptm/m/n/10
: This en-ables typ-i-cal
Underfull \hbox (badness 4556) in paragraph at lines 5376--5383
[]\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : T
he list must have two
[2380]
Underfull \hbox (badness 3302) in paragraph at lines 5401--5404
[]\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 :
re-turn the kro-necker
[2381] [2382] [2383] [2384]
Overfull \hbox (138.78088pt too wide) in paragraph at lines 5776--5776
[]\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, tol1 = 8
* tol, checkDN = TRUE, ...)[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5782--5782
[]\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, checkDN
= TRUE, ...)[]
[2385]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5841--5841
[]\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if
not "formally"[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5845--5845
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g
eneric from base[]
[2386]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5937--5937
[]\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even
if not "formally"[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5962--5962
[]\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames
= FALSE)
[2387] [2388]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042
[]\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 6043--6043
[] \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 6050--6050
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2389] [2390]
Underfull \hbox (badness 1062) in paragraph at lines 6204--6207
[]\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 6233--6236
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2391]
Underfull \hbox (badness 2635) in paragraph at lines 6402--6407
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ldenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6402--6407
\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 "Matri
x"[]\T1/ptm/m/n/10 , by class
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 6410--6413
[]\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.,
Underfull \hbox (badness 10000) in paragraph at lines 6566--6576
[]\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T
1/ptm/m/n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6566--6576
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc
r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10
, and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\
T1/ptm/m/n/10 --in
[2393]
Underfull \hbox (badness 3179) in paragraph at lines 6648--6651
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2394]
Underfull \hbox (badness 10000) in paragraph at lines 6751--6754
[]\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.,
[2395]
Underfull \hbox (badness 10000) in paragraph at lines 6830--6833
[]\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.,
[2396]
Underfull \hbox (badness 1430) in paragraph at lines 6904--6910
\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, []\T1/pcr/
m/n/10 lu(x,
[2397]
Underfull \hbox (badness 1675) in paragraph at lines 6929--6932
[]\T1/pcr/m/n/10 lu() []\T1/ptm/m/n/10 is a generic func-tion with spe-cial met
h-ods for dif-fer-ent types of ma-tri-ces. Use
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7001--7001
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2398] [2399]
Underfull \hbox (badness 10000) in paragraph at lines 7141--7144
[]\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm
/m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x
,
[2400]
Underfull \hbox (badness 1490) in paragraph at lines 7163--7165
[]\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/
m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][
] []\T1/ptm/m/n/10 and (one case of)
[2401] [2402]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again>
\relax
l.7358 \aliasA{det}{Matrix-class}{det}
[2403pdfTeX warning (ext4): destination
with the same identifier (name{Rfn.coerce,Matrix,denseMatrix.Rdash.method}) has
been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.7439 \item[dim]
\code{signature(x = "Matrix")}: extract matrix dimensions]
Underfull \hbox (badness 1337) in paragraph at lines 7446--7449
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set
the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a
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Underfull \hbox (badness 10000) in paragraph at lines 7469--7471
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This
re-lies on a cor-rect
[2404]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.7532 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again>
\relax
l.7629 ...A{crossprod}{matrix-products}{crossprod}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again>
\relax
l.7723 ...tcrossprod}{matrix-products}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 7816--7822
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/
pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2405]
Underfull \hbox (badness 10000) in paragraph at lines 7889--7892
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 10000) in paragraph at lines 7892--7897
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
Underfull \hbox (badness 3557) in paragraph at lines 7892--7897
[]\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr
ix mul-ti-pli-ca-tion. Mul-ti-
Underfull \hbox (badness 6608) in paragraph at lines 7897--7901
\T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas
s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 1552) in paragraph at lines 7907--7908
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-
[2406] [2407] [2408]
Underfull \hbox (badness 1062) in paragraph at lines 8087--8090
[]\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 8121--8124
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2409]
Underfull \hbox (badness 3312) in paragraph at lines 8177--8179
[]\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 []\T1/pcr/m/n/10 X <-
[2410] [2411]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 8279--8279
[] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 8319--8319
[]\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 [2412]
Underfull \hbox (badness 2635) in paragraph at lines 8386--8391
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ndenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 8386--8391
\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 "Matri
x"[]\T1/ptm/m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 8394--8397
[]\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.,
[2413]
Underfull \hbox (badness 2521) in paragraph at lines 8464--8470
[]\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N
ote that these co-er-cions
[2414]
Underfull \hbox (badness 1867) in paragraph at lines 8586--8588
[]\T1/ptm/m/n/10 fast sim-
[2415]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8626 \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
<to be read again>
\relax
l.8626 \HeaderA{norm}{Matrix Norms}{norm}
[2416]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8719--8719
[]\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 8720--8720
[]\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 8721--8721
[]\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 8867--8877
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n
/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri
x[]\T1/ptm/m/n/10 ,
[2417]
Underfull \hbox (badness 3179) in paragraph at lines 8938--8941
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2418]
Underfull \hbox (badness 10000) in paragraph at lines 9036--9039
[]\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.,
[2419]
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[]\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.,
[2420] [2421]
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op =
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[2423]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") []\T1/ptm/m/n/10 and ot
her sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "integer", to = "pMatrix")[]\T1/ptm/m/n/10 :
This is en-ables typ-i-cal
[2424]
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "matrix")[]\T1/ptm/m/n/10 : c
o-er-cion to a tra-di-tional
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[]\T1/pcr/m/n/10 signature(x = "pMatrix", logarithm="logical")[]\T1/ptm/m/n/10
: Since per-mu-ta-
Underfull \hbox (badness 3229) in paragraph at lines 9354--9358
\T1/ptm/m/n/10 trix; note that []\T1/pcr/m/n/10 solve(P) []\T1/ptm/m/n/10 is id
en-ti-cal to []\T1/pcr/m/n/10 t(P) []\T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-c
es. See
[2425]
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[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of []
\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2426] [2427]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.9569 \aliasA{qr}{qr-methods}{qr}
[2428]
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[]\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![]
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[]\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[]
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[]\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[]
[2429]
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[]\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10
qr[][][](x, tol,
[2430]
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 , it cor-re-sponds to
[2431]
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[]\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"[]
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[]\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol
= 1e-7)) # all 14[]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war
ning+ ~1.5 sec (2013)[]
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[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
[2432]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rco
nd}) has been already used, duplicate ignored
<to be read again>
\relax
l.9893 ... the Reciprocal Condition Number}{rcond}
[2433]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2434] [2435] [2436]
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\T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr
ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n
/10 is not
[2437] [2438]
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class []\T1/pcr/m/n
/10 "Matrix"[]\T1/ptm/m/n/10 ) or tra-di-tional
[2439]
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[] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[]
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[]\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[]
[2440]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.10470 \aliasA{solve}{solve-methods}{solve}
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[]\T1/pcr/m/n/10 ## solve(a, b, ...) # the two-argument version, almost always
preferred to
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[]\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "
D", "P", "Pt"), ...)[]
[2441]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 solve []\T1/ptm/m/n/10 meth-ods for a
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[]\T1/ptm/m/n/10 (for all []\T1/pcr/m/n/10 b[]\T1/ptm/m/n/10 ) work via []\T1/p
cr/m/n/10 as(a,
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 (
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 (
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\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-met-ric,
[2442]
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
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[]\T1/ptm/m/n/10 works via []\T1/pcr/m/n/10 as(b,
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via []\T1/pcr/m/n/10 as(a,
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[][][]\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
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 sparseLU[][][][]\T1/ptm/m/n/10 ,
and
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[]\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2443]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs
parse)[]
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs
parse,[]
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[]\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,
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[]\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)
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[]\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c
on-trasts to be ap-plied to the
[2444]
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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[]\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
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2445]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2446] [2447]
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[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
[2448]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2449]
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[]\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
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[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
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[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2450]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\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)[]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[]
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[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
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[]\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\
T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods
[2452]
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[][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences,
such 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
<to be read again>
\relax
l.11486 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2453] [2454]
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[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")[]\T1/ptm/m/n/10 : For []\
T1/pcr/m/n/10 solve(a,b)[]\T1/ptm/m/n/10 , sim-ply uses
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[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
[2455]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
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[]\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-
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\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 "
lsparseVector"[]\T1/ptm/m/n/10 ,
[2456]
Underfull \hbox (badness 10000) in paragraph at lines 11834--11837
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/
n/10 co-erces sparse
[2457]
Underfull \hbox (badness 10000) in paragraph at lines 11874--11879
[]\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 11889--11891
[][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str
uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*,
[2458] [2459]
Underfull \hbox (badness 2310) in paragraph at lines 12014--12020
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more
usual con-struc-tor of such ma-tri-ces. Then,
[2460]
Underfull \hbox (badness 6188) in paragraph at lines 12105--12107
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix", to = "symmetricMatrix")[]\T1/ptm
/m/n/10 : and many
[2461]
Underfull \hbox (badness 2591) in paragraph at lines 12131--12136
\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-m
eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
Underfull \hbox (badness 2057) in paragraph at lines 12207--12209
[]\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.,
[2462] [2463]
Underfull \hbox (badness 6641) in paragraph at lines 12294--12297
[]\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 ) h
ave meth-ods with
Underfull \hbox (badness 5133) in paragraph at lines 12338--12342
[]\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 12338--12342
\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
[2464] [2465]
Underfull \hbox (badness 7649) in paragraph at lines 12445--12447
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2466] [2467]
Underfull \hbox (badness 10000) in paragraph at lines 12563--12565
[]\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 ,
though
[2468]
Underfull \hbox (badness 1668) in paragraph at lines 12692--12695
[][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac
k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac
kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes
[2469]
Underfull \hbox (badness 7362) in paragraph at lines 12743--12745
[]\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
[2470]
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[]\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 12782--12782
[]\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)[]
[2471] [2472]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12936--12936
[] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/
x))$modulus))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12941--12941
[] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/
x))$modulus))[]
[2473]
Underfull \hbox (badness 6910) in paragraph at lines 13147--13149
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2474]
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref) removing `\Rpercent' on input line 13194.
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref) removing `\Rpercent' on input line 13194.
[2475]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13312--13312
[]\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero
s" to drop0()[]
[2476]) (./boot-pkg.tex
Chapter 18.
[2477] [2478] [2479] [2480] [2481] [2482] [2483]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532
[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2484]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\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 585--590
[]\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-
[2485] [2486] [2487]
Underfull \hbox (badness 1881) in paragraph at lines 826--828
[]\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 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo
ot.ci[][][][]\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 j
ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T
1/ptm/m/n/10 ,
[2488]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887
[]\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 [2489]
[2490] [2491]
Underfull \hbox (badness 1496) in paragraph at lines 1084--1093
[]\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 1084--1093
\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 1084--1093
\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 1105--1111
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2492] [2493] [2494] [2495]
Underfull \hbox (badness 1571) in paragraph at lines 1445--1447
[]\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-
[2496] [2497] [2498] [2499] [2500]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2501] [2502] [2503]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2505]
Underfull \hbox (badness 6268) in paragraph at lines 2084--2086
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2506] [2507] [2508]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\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
[2509]
Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat
istic []\T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2432--2434
[]\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 2440--2441
[][][]\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 ,
[2510] [2511]
Underfull \hbox (badness 1077) in paragraph at lines 2536--2540
[]\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/1
0 is the sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2536--2540
\T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr
/m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T
1/ptm/m/n/10 is used. This is mul-ti-plied by
[2512] [2513] [2514] [2515] [2516]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
[]\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 2897--2897
[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2517] [2518] [2519]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr
ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/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 ,
[2520]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2521] [2522] [2523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2524] [2525] [2526] [2527] [2528] [2529] [2530]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2531] [2532]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2533] [2534] [2535] [2536]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2537] [2538]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\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 4371--4375
\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the
r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a
re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to
[2539] [2540] [2541] [2542] [2543] [2544] [2545] [2546] [2547]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2548] [2549] [2550] [2551]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\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 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2552]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2561]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
[]\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less
than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then
[2562]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s
addle.distn"[]\T1/ptm/m/n/10 . See the help file for
[2563] [2564] [2565] [2566]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
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[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2569] [2570] [2571]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\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
[2572] [2573]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2574] [2575] [2576] [2577] [2578] [2579] [2580] [2581]) (./class-pkg.tex
[2582]
Chapter 19.
[2583] [2584] [2585] [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593]
[2594] [2595] [2596] [2597] [2598]) (./cluster-pkg.tex
Chapter 20.
[2599] [2600] [2601]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
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[] \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 255--255
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2602] [2603]
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[2605]
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[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
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[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2606] [2607]
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[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
[2608]
Underfull \hbox (badness 3078) in paragraph at lines 691--694
[]\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
[2609] [2610]
Underfull \hbox (badness 2941) in paragraph at lines 791--794
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\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 ,
[2611]
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[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2612]
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[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2613]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2614] [2615]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1121--1121
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
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[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 1176--1176
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
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[]\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
[2617]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1284--1284
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
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[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2618] [2619] [2620]
Underfull \hbox (badness 10000) in paragraph at lines 1477--1480
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[][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds
cale[][][][]\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/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1518--1518
[]\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 1528--1528
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2621]
Underfull \hbox (badness 5741) in paragraph at lines 1568--1571
[]\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d
er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2622]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1637--1637
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2623]
Underfull \hbox (badness 1552) in paragraph at lines 1686--1688
[]\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n
/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se
e
Underfull \hbox (badness 1629) in paragraph at lines 1699--1703
[]\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault
\T1/ptm/m/n/10 for all nu-meric
Underfull \hbox (badness 3746) in paragraph at lines 1699--1703
\T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T
1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r
e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see
[2624]
Underfull \hbox (badness 1540) in paragraph at lines 1775--1783
\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 $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 =
[2625]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1867--1867
[]\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1886--1886
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2626] [2627] [2628] [2629] [2630]
Underfull \hbox (badness 10000) in paragraph at lines 2207--2210
Underfull \hbox (badness 3179) in paragraph at lines 2221--2227
[][][]\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/1
0 ellipsoid []\T1/ptm/m/n/10 ob-jects.
[2631] [2632]
Underfull \hbox (badness 10000) in paragraph at lines 2379--2382
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2633]
Underfull \hbox (badness 1292) in paragraph at lines 2447--2450
[]\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10
, the num-ber of it-er-a-tions needed and
[2634]
Underfull \hbox (badness 6675) in paragraph at lines 2456--2458
[]\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 2479--2482
[][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f
anny[][][][]\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 ,
[2635] [2636]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 2608--2608
[]\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES
= FALSE, ...)
[2637]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 2655--2655
[] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k
<= k, table(cl.k) >= 2)[]
[2638]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2760--2760
[]\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 ):[]
[2639]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2839--2839
[] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[]
[2640] [2641] [2642]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2643] [2644]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3171--3171
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2645] [2646] [2647]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3367--3367
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3368--3368
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2648]
Underfull \hbox (badness 10000) in paragraph at lines 3435--3438
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m
/n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <-
[2649]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3485--3485
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3486--3486
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2650] [2651] [2652]
Underfull \hbox (badness 10000) in paragraph at lines 3671--3674
[]\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 [][][]\T1/pcr/m/n/10 pam[]
[][](*,
Underfull \hbox (badness 1448) in paragraph at lines 3671--3674
\T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p
tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is
[2653]
Underfull \hbox (badness 10000) in paragraph at lines 3734--3739
[][][]\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.de
fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 ,
[2654]
Underfull \hbox (badness 1748) in paragraph at lines 3796--3801
\T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p
tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx
<-
Underfull \hbox (badness 6268) in paragraph at lines 3808--3811
[][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o
bject[][][][]\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/1
0 hclust[][][][]\T1/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 ,
[2655] [2656] [2657]
Underfull \hbox (badness 10000) in paragraph at lines 3993--3996
[][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag
nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4024--4027
[][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl
ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2658]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4077--4077
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
[2659]
Underfull \hbox (badness 2035) in paragraph at lines 4088--4090
[]\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
[2660] [2661] [2662]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4281--4281
[] \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 4283--4283
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2663] [2664]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4426--4426
[]\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 4435--4435
[] \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 4437--4437
[] \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 4440--4440
[]\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 4442--4442
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4449--4449
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2665] [2666] [2667] [2668] [2669] [2670] [2671]
Underfull \hbox (badness 10000) in paragraph at lines 4823--4829
[]\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i
s slightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4839--4841
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4852--4852
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4854--4854
[]\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s medoid indices == pam(xclara, 3)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4864--4864
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2672]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4868--4868
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2673]) (./codetools-pkg.tex [2674]
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2675]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage
Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2676]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2677] [2678] [2679]) (./foreign-pkg.tex [2680]
Chapter 22.
Underfull \hbox (badness 10000) in paragraph at lines 33--37
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2681]
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
[2682] [2683]
Underfull \hbox (badness 3601) in paragraph at lines 237--245
[]\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 ,
[2684]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295
[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2685] [2686] [2687]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2688]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462
[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 2846) in paragraph at lines 505--514
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-ent lev-
Underfull \hbox (badness 3746) in paragraph at lines 505--514
\T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul
t), the first orig-i-nal value la-bel is
Underfull \hbox (badness 2269) in paragraph at lines 505--514
\T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p
cr/m/n/10 paste0(label,
Underfull \hbox (badness 10000) in paragraph at lines 515--518
[]\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 515--518
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup
licated_"[]\T1/ptm/m/n/10 ) if
[2689]
Underfull \hbox (badness 10000) in paragraph at lines 550--558
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com /
en-[]us / windows / win32 / intl /
Underfull \hbox (badness 7613) in paragraph at lines 568--574
[]\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute
[2690]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623
[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624
[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2691]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657
[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 661--661
[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2692] [2693]
Underfull \hbox (badness 10000) in paragraph at lines 812--813
Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2694]
Underfull \hbox (badness 10000) in paragraph at lines 869--873
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 869--873
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 869--873
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 869--873
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2695]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 900--900
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2696]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2697] [2698]
Underfull \hbox (badness 10000) in paragraph at lines 1076--1077
[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase
/ format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2699] [2700]
Underfull \hbox (badness 10000) in paragraph at lines 1270--1276
[]\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig
n:::writeForeignStata[]\T1/ptm/m/n/10 ,
[2701]
Underfull \hbox (badness 2088) in paragraph at lines 1296--1299
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid
e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET
[2702]) (./lattice-pkg.tex
Chapter 23.
[2703]
Underfull \hbox (badness 2073) in paragraph at lines 117--121
\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
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\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm /
ms / departments / sia /
[2704] [2705]
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"),[]
[2706]
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[] \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"),[]
[2707] [2708] [2709] [2710]
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
[2711] [2712] [2713] [2714]
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
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2715]
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 sho
uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2716] [2717]
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
[2718] [2719] [2720]
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 ,
[2721]
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/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 ,
[2722]
Underfull \vbox (badness 10000) has occurred while \output is active [2723]
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
[2724]
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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T
1/ptm/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
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
[2725] [2726] [2727] [2728]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
[2729]
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-fie
d, the 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 firs
t checked. If
[2730] [2731] [2732]
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"),[]
[2733] [2734] [2735] [2736] [2737]
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"),[]
[2738] [2739]
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/
pcr/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/ptm/m/n/10 must have the same lengths as
[2740]
Underfull \hbox (badness 6758) in paragraph at lines 2919--2923
[]\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 2919--2923
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra
ster[][][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2925--2927
[]\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][]
[]\T1/ptm/m/n/10 when
Underfull \hbox (badness 1609) in paragraph at lines 2977--2983
[]\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 2977--2983
\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 2977--2983
\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
[2741]
Underfull \hbox (badness 2486) in paragraph at lines 3001--3005
[]\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
[2742]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3104--3104
[] \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 3105--3105
[] \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 3106--3106
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
[2743]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3129--3129
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2744]
Underfull \hbox (badness 2913) in paragraph at lines 3187--3194
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3187--3194
[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
[2745] [2746] [2747]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3475 \aliasA{parallel}{B\_08\_splom}{parallel}
[2748]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3517--3517
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2749] [2750] [2751] [2752] [2753]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3876--3876
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2754] [2755]
Underfull \hbox (badness 2277) in paragraph at lines 3970--3974
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault
set-tings by
Underfull \hbox (badness 2435) in paragraph at lines 3970--3974
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2756]
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[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
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[]\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
[2757]
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[]\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 4153--4157
[]\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren
t set-tings (ob-tained by
[2758]
Underfull \hbox (badness 5161) in paragraph at lines 4218--4222
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell
is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4218--4222
\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
[2759] [2760]
Underfull \hbox (badness 1067) in paragraph at lines 4336--4346
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/
10 is 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 4336--4346
[]\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 4336--4346
[]\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super
pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4336--4346
[]\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used
only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4336--4346
[]\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/
n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10
for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl
ot.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 4364--4366
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10
plot.polygon []\T1/ptm/m/n/10 and
[2761] [2762] [2763] [2764] [2765]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4768--4768
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2766] [2767]
Underfull \vbox (badness 1092) has occurred while \output is active [2768]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4958
[]\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 .
[2769] [2770]
Underfull \hbox (badness 1442) in paragraph at lines 5087--5090
[]\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle
s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and
[2771] [2772] [2773] [2774] [2775]
Underfull \hbox (badness 3646) in paragraph at lines 5426--5429
[][][]\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-call
y the en-try for
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[] \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 5457--5457
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2776]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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[]\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the
left of pan-els us-ing
[2777]
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[]\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect,
which is to draw a strip ap-pro-pri-ate for
[2778] [2779]
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[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
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[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
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[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
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[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
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[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
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[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
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[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5752--5752
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
[2780]
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[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2781]
Underfull \hbox (badness 2538) in paragraph at lines 5907--5911
\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul
t 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 5918--5925
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e
x-tra pa-ram-e-ters are passed on to
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[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the
se are used (in com-bi-na-tion with
[2782] [2783]
Underfull \hbox (badness 10000) in paragraph at lines 6071--6075
[][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt
ice[][][][]\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 ,
[2784]
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[2786]
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[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2787] [2788]
Underfull \hbox (badness 3601) in paragraph at lines 6334--6339
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m
/n/10 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 6334--6339
\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa
ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2789]
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[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2790] [2791]
Underfull \hbox (badness 1888) in paragraph at lines 6553--6560
[]\T1/pcr/m/n/10 at []\T1/ptm/m/n/10 can be a nu-meric vec-tor, []\T1/pcr/m/n/1
0 col.regions []\T1/ptm/m/n/10 a vec-tor of col-ors, and
[2792]
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[]\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 6610--6613
[]\T1/pcr/m/n/10 shade.colors.palette []\T1/ptm/m/n/10 func-tion should re-turn
a valid color. The
[2793] [2794] [2795] [2796] [2797]
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[]\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p
anel func-tion that uses the raster draw-
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\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
[2798] [2799]
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[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
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[]\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi
s func-tion is passed
[2800] [2801]
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\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
[2802] [2803]
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2804]
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[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2805] [2806]
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[]\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed o
n to
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[]\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b
e a list of ar-gu-ments to be sup-plied to
[2807]
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[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
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[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2808]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
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[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2809] [2810] [2811]
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[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
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[]\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
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super
pose
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[]\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
[2820] [2821]
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[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
[2822]
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[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
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[]\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
[2823]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2824] [2825]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2826]
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[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2827] [2828]
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[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2829]
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\T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r
ight.x, right.y, left.name, right.x.name,
[2830] [2831] [2832] [2833] [2834] [2835] [2836]
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[]\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1
0 , []\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 ,
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[]\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4
57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 ,
[2837] [2838] [2839]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9923 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2840] [2841] [2842]
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\T1/pcr/m/n/10 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 , []\T1/pcr/m/n/10 He
art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower
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[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2843] [2844]) (./mgcv-pkg.tex
Chapter 24.
[2845] [2846]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
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[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2847]
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[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2848] [2849] [2850] [2851]
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[][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\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 ,
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[][][]\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
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2852]
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2853] [2854] [2855]
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[]\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog"
[]\T1/ptm/m/n/10 and
[2856] [2857]
Underfull \hbox (badness 1406) in paragraph at lines 704--705
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2858] [2859]
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[]\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
[2860]
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[]\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).
[2861]
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[2863] [2864] [2865] [2866] [2867] [2868] [2869]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
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[] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[]
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[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[]
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[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[]
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[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
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[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
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[2872]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
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[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
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[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
[2874] [2875] [2876] [2877] [2878] [2879]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1937--1937
[]\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di
screte=TRUE)[]
[2880] [2881] [2882] [2883]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2884] [2885] [2886] [2887] [2888] [2889] [2890]
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
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[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n
/10 formula.gam[][][] []\T1/ptm/m/n/10 and also
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2891] [2892] [2893]
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\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
[2894] [2895]
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[][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\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
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2896]
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[2900] [2901]
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[]\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1
e-07, maxit = 200,
[2902] [2903] [2904] [2905] [2906] [2907]
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[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
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[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
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[] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU
LL,...)[]
[2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915]
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[]\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
[2916] [2917]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[] \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)+[]
[2928] [2929] [2930]
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[]\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0,
d1b = 0,
[2931] [2932]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2933]
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[]\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver-
gence fail-ures, con-sider mod-i-fy-ing
[2934] [2935]
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[][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor
-re-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 ,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n
egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1
0 ,[][][]\T1/pcr/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 .
[2936]
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[2938] [2939] [2940]
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[]\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
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2941] [2942] [2943] [2944] [2945] [2946] [2947]
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(..
.,fit=FALSE) []\T1/ptm/m/n/10 or
[2948] [2949]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
[2950]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
[2951] [2952]
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[] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[]
[2953] [2954] [2955] [2956] [2957]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
[2958]
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[]\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2959] [2960] [2961]
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[2963] [2964]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 6914--6914
[]\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE)
[2965] [2966] [2967] [2968]
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[2971] [2972]
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 7373--7373
[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
[2973] [2974] [2975] [2976] [2977] [2978] [2979] [2980] [2981]
Underfull \hbox (badness 1242) in paragraph at lines 7916--7917
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2982] [2983]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8003--8003
[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2984] [2985]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8066--8066
[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[2998] [2999] [3000] [3001] [3002] [3003]
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[3005]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim
.pdIndot[]\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 9310--9313
[]\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd
Idnot[]\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 9310--9313
[]\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p
dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 .
[3006]
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[]\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p
dTens[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n
ot nor-mally be
[3007] [3008] [3009]
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[]
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[] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[]
[3010] [3011] [3012]
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[]\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
[3013] [3014] [3015] [3016]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,gc.level=0,...)[]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para-
[3017] [3018] [3019]
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
[3020] [3021]
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[]\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi
nal grid points[]
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[]\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1)
,x3=rep(0,n))[]
[3022]
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[] \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[]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\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
[3025]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
[3026]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al
-though 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,
[3027] [3028] [3029]
Underfull \hbox (badness 1253) in paragraph at lines 10738--10740
[]\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,
[3030] [3031] [3032] [3033] [3034]
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[]\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
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\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 10991--10998
\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: see
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n
/10 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 10999--11002
\T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s
mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[3035]
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[]
[3036]
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[]\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 ,
[3037] [3038] [3039] [3040] [3041]
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[]\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)
[3042] [3043] [3044] [3045] [3046] [3047]
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[] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
+ (eps/del))[]
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[]\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[]
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[3049]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
model ma-trix X, or, if
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[]\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE,
cov = TRUE,[]
[3050]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
[3051] [3052] [3053]
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[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
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[]\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
[3054]
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\T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10
vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n
/10 "NA"[]\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w
ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec
[3055]
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[]\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 12225--12229
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc
r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 ,
[3056] [3057] [3058]
Underfull \hbox (badness 6876) in paragraph at lines 12420--12426
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on
e or two vari-ables, spec-i-fied via terms like
[3059]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3060] [3061]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3062]
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[] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[]
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[] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[]
[3063]
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[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
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[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
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[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
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[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[3064]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
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\T1/ptm/m/n/10 term []\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
[3065] [3066]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3067] [3068]
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[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
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[]\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[]
[3069] [3070]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3071] [3072] [3073] [3074] [3075]
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[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3076]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3077] [3078]
Underfull \hbox (badness 10000) in paragraph at lines 13573--13576
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met
hod a smooth spec-i-fi-ca-tion ob-
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\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 13573--13576
[]\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"
[3079] [3080]
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[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3081]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
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[]\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-
[3082] [3083] [3084]
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[]\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...[]
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[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th
e sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14047--14048
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3087] [3088] [3089]
Underfull \hbox (badness 7613) in paragraph at lines 14192--14195
[]\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [
]\T1/ptm/m/n/10 pro-duced by the
[3090]
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[]\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a
sin-gle smooth-ing pa-ram-e-
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[]\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs
="sz",id=1),data=dat,method="REML")[]
[3091] [3092] [3093]
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[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an
y num-ber of vari-ables, spec-i-fied via terms like
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3094] [3095] [3096] [3097] [3098] [3099]
Underfull \hbox (badness 10000) in paragraph at lines 14741--14743
[]\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see
Underfull \hbox (badness 10000) in paragraph at lines 14771--14775
[][][]\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 14771--14775
[][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 soap[][][
][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical.Spline[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14771--14775
[][][]\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 ,
[3100] [3101] [3102] [3103] [3104]
Underfull \hbox (badness 2158) in paragraph at lines 15061--15061
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3105] [3106]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15140--15140
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3107] [3108]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 15274--15274
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3109] [3110]
Underfull \hbox (badness 4846) in paragraph at lines 15405--15408
[]\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
[3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121]
[3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130]
Overfull \hbox (120.78088pt too wide) in paragraph at lines 16623--16623
[]\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL,
unconditional=FALSE, ...)[]
[3131]
Underfull \hbox (badness 1715) in paragraph at lines 16645--16646
[]\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object
$Vc []\T1/ptm/m/n/10 (if avail-able) from a
[3132] [3133] [3134]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 16835--16835
[]\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1,
Overfull \hbox (48.78088pt too wide) in paragraph at lines 16837--16837
[]\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16839--16839
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 16859--16860
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 16859--16860
[]\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le
cted by []\T1/pcr/m/n/10 ar.row
[3136]
Underfull \vbox (badness 10000) has occurred while \output is active [3137]
[3138]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17047--17047
[]\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 17048--17048
[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
[3139]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17060--17060
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[3140] [3141] [3142]) (./nlme-pkg.tex
Chapter 25.
[3143]
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
- fit-ted) are used; else, if
[3144]
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
- fit-ted) are used; else, if
[3145] [3146] [3147] [3148] [3149]
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,[]
[3150] [3151]
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 ---------------------------
---------------[]
[3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159]
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"),[]
[3160]
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
.htm[]\T1/ptm/m/n/10 ', the first edi-tion of
[3161] [3162] [3163] [3164] [3165] [3166] [3167]
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.
effects.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
,
[3168]
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
[3169] [3170] [3171] [3172] [3173]
Underfull \hbox (badness 2042) in paragraph at lines 1996--2002
\T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10
group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 ,
[3174]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[3175]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3176] [3177]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR
MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 ,
[3178]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186]
Underfull \hbox (badness 10000) in paragraph at lines 2849--2853
[][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor
Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[
][][][]\T1/ptm/m/n/10 ,
[3187] [3188] [3189] [3190] [3191] [3192pdfTeX warning (ext4): destination with
the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d
uplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE)
] [3193] [3194] [3195]
[3196] [3197] [3198]
Underfull \hbox (badness 6493) in paragraph at lines 3585--3593
[][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau
s[][][][]\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 corSp
her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T
1/ptm/m/n/10 ,
[3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209]
[3210] [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220]
[3221] [3222]
Underfull \hbox (badness 10000) in paragraph at lines 5165--5169
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p
cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 ,
[3223] [3224] [3225] [3226] [3227] [3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5597--5600
[][][]\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 ,
[3230] [3231] [3232] [3233] [3234] [3235] [3236] [3237] [3238]
Underfull \hbox (badness 2799) in paragraph at lines 6103--6109
\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
[3239]
Underfull \hbox (badness 7133) in paragraph at lines 6164--6168
[]\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 ,
[3240]
Underfull \hbox (badness 2057) in paragraph at lines 6253--6264
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl
sControl[][][][]\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 ,
[3241]
Underfull \hbox (badness 10000) in paragraph at lines 6317--6319
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3242] [3243] [3244] [3245]
Underfull \hbox (badness 7133) in paragraph at lines 6566--6570
[]\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 ,
[3246]
Underfull \hbox (badness 10000) in paragraph at lines 6665--6671
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn
lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6692--6692
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3247]
Underfull \hbox (badness 10000) in paragraph at lines 6730--6732
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3248] [3249] [3250] [3251]
Underfull \hbox (badness 10000) in paragraph at lines 7002--7009
[][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl
y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff
GroupedData[][][][]\T1/ptm/m/n/10 ,
[3252]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7020--7020
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7025--7025
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7047--7049
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr
oupedData []\T1/ptm/m/n/10 ob-ject or a
[3253] [3254] [3255]
Underfull \hbox (badness 10000) in paragraph at lines 7262--7267
[][][]\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 Initi
alize.glsStruct[][][][]\T1/ptm/m/n/10 ,
[3256] [3257] [3258]
Underfull \hbox (badness 1997) in paragraph at lines 7414--7422
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-tion and op-ti-
Underfull \hbox (badness 2205) in paragraph at lines 7414--7422
\T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n
/10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20,
Underfull \hbox (badness 3118) in paragraph at lines 7437--7440
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ
e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/
n/10 ,
[3259] [3260] [3261]
Underfull \hbox (badness 3354) in paragraph at lines 7653--7655
[]\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
[3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269]
Underfull \hbox (badness 10000) in paragraph at lines 8170--8187
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm
e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8170--8187
[][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL
ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\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 8213--8213
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
[3270]
Underfull \hbox (badness 1642) in paragraph at lines 8222--8244
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3271] [3272] [3273] [3274]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8487--8487
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8535--8537
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3275]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8579--8579
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286]
[3287]
Underfull \hbox (badness 10000) in paragraph at lines 9336--9343
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9347--9347
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3288] [3289] [3290] [3291] [3292]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9698 ...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
<to be read again>
\relax
l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3293]
Underfull \hbox (badness 10000) in paragraph at lines 9718--9721
[]\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 9762--9765
[]\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 9762--9765
\T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10
. Must have the same di-men-sions as
[3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] [3304]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10442--10442
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3305]
Underfull \hbox (badness 1596) in paragraph at lines 10471--10497
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3306] [3307] [3308]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10647--10647
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3309] [3310]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10798--10798
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10809--10814
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi
nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [
][][]\T1/pcr/m/n/10 nlm[][][]
[3311]
Underfull \hbox (badness 6961) in paragraph at lines 10831--10835
[]\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p
tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control=
Underfull \hbox (badness 10000) in paragraph at lines 10850--10852
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3312] [3313] [3314] [3315]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11141--11141
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11142--11142
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
[3316] [3317] [3318] [3319] [3320] [3321]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11532--11532
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3322] [3323] [3324] [3325] [3326] [3327]
Underfull \hbox (badness 6268) in paragraph at lines 11919--11929
[][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\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[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 ,
[3328] [3329] [3330] [3331]
Underfull \hbox (badness 10000) in paragraph at lines 12180--12186
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 ,
[3332] [3333] [3334] [3335] [3336]
Underfull \hbox (badness 6876) in paragraph at lines 12502--12504
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/
10 ini-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
[3337] [3338]
Underfull \hbox (badness 2452) in paragraph at lines 12658--12665
[][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\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 ,
[3339]
Underfull \hbox (badness 10000) in paragraph at lines 12723--12729
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 ,
[3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13312--13312
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3349] [3350] [3351] [3352] [3353]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13677--13677
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3354]
Underfull \hbox (badness 10000) in paragraph at lines 13704--13707
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3355]
Underfull \hbox (badness 1838) in paragraph at lines 13747--13754
[]\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 13747--13754
[]\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
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13804--13804
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3356]
Underfull \hbox (badness 10000) in paragraph at lines 13811--13814
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13811--13814
[]\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary
co-vari-ate and a sin-gle
[3357]
Underfull \hbox (badness 10000) in paragraph at lines 13919--13922
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped
Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3358] [3359]
Underfull \hbox (badness 10000) in paragraph at lines 14013--14015
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c
ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe
dData[][][][]\T1/ptm/m/n/10 ,
[3360] [3361] [3362] [3363] [3364] [3365] [3366] [3367]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14537--14537
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3368] [3369] [3370] [3371] [3372] [3373] [3374] [3375] [3376]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been
already used, duplicate ignored
<to be read again>
\relax
l.15190 ...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
<to be read again>
\relax
l.15190 ...Extract Random Effects}{random.effects}
[3377] [3378] [3379]
[3380] [3381] [3382] [3383] [3384] [3385] [3386]
Underfull \hbox (badness 2126) in paragraph at lines 15830--15834
[]\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199
7). Phar-ma-coki-net-
[3387]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15838--15838
[]\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15857--15857
[] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718
4, tol = 1.5e-5),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15858--15858
[] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),
tol = 7e-7)[]
[3388]
Underfull \hbox (badness 1009) in paragraph at lines 15888--15897
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3389] [3390]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16035--16035
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3391] [3392] [3393] [3394] [3395]
Underfull \hbox (badness 10000) in paragraph at lines 16370--16376
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l
me[][][][]\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.reStruct[][][][]\T1/ptm/m/n/10 ,
[3396]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16401--16401
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3397] [3398] [3399] [3400] [3401] [3402] [3403]
Underfull \hbox (badness 1728) in paragraph at lines 16889--16892
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3404] [3405] [3406] [3407] [3408]
Underfull \hbox (badness 1803) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite,
Underfull \hbox (badness 10000) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p
dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General
Underfull \hbox (badness 7888) in paragraph at lines 17223--17232
\T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[
]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object)
[3409]
Underfull \hbox (badness 10000) in paragraph at lines 17294--17295
[]\T1/pcr/m/n/10 "Constant plus power of variance
Underfull \hbox (badness 10000) in paragraph at lines 17295--17296
[]\T1/pcr/m/n/10 "Constant plus proportion of variance
[3410] [3411] [3412] [3413]
Underfull \hbox (badness 10000) in paragraph at lines 17545--17553
[][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo
nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p
tm/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 ,
[3414] [3415] [3416] [3417]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17817--17817
[]\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17819--17819
[]\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[]
[3418] [3419] [3420] [3421] [3422] [3423]
Underfull \hbox (badness 10000) in paragraph at lines 18255--18265
[][][]\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.co
rLin[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18255--18265
[][][]\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 Variogr
am.corSpher[][][][]\T1/ptm/m/n/10 ,
[3424]
Underfull \hbox (badness 3579) in paragraph at lines 18293--18298
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3425]
Underfull \hbox (badness 3579) in paragraph at lines 18357--18362
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3426]
Underfull \hbox (badness 3579) in paragraph at lines 18420--18425
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3427]
Underfull \hbox (badness 1577) in paragraph at lines 18481--18483
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR
atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18483--18488
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3428]
Underfull \hbox (badness 3579) in paragraph at lines 18546--18551
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18579--18588
[][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va
riogram[][][][]\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 18579--18588
[][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rRatio[][][][]\T1/ptm/m/n/10 ,
[3429]
Underfull \hbox (badness 3579) in paragraph at lines 18618--18623
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3430] [3431]
Underfull \hbox (badness 1009) in paragraph at lines 18764--18773
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3432] [3433]
Underfull \hbox (badness 1009) in paragraph at lines 18896--18905
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
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ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
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\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3443]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3444] [3445] [3446]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3447]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428
[]\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 431--431
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3448] [3449]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3450]) (./rpart-pkg.tex
Chapter 27.
[3451] [3452] [3453] [3454]
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, ...)[]
[3455] [3456] [3457] [3458]
Underfull \hbox (badness 1442) in paragraph at lines 592--598
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil
l be at the hor-i-zon-tal plot co-or-di-nates of
[3459] [3460]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
Underfull \hbox (badness 10000) in paragraph at lines 771--775
[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
adds to the la-bel
Underfull \hbox (badness 1142) in paragraph at lines 771--775
\T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [
]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n
[3461] [3462] [3463]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915
[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"),[]
[3464] [3465] [3466] [3467]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180
[]\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 1181--1181
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2846) in paragraph at lines 1243--1245
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n
/10 rpart []\T1/ptm/m/n/10 al-go-rithm. See
[3468]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287
[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\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 1304--1304
[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3469] [3470] [3471] [3472] [3473] [3474] [3475]
Underfull \hbox (badness 1565) in paragraph at lines 1760--1763
[]\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 ',
[3476]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3477] [3478] [3479]) (./spatial-pkg.tex [3480]
Chapter 28.
[3481] [3482] [3483] [3484] [3485] [3486]
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[3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497]
[3498] [3499]) (./survival-pkg.tex [3500]
Chapter 29.
[3501] [3502]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
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[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3503] [3504]
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[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as
long as
[3505] [3506]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again>
\relax
l.384 ... 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
<to be read again>
\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
[3507]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
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[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3508]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3509] [3510] [3511]
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[]\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival
[3512]
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3513] [3514]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3515] [3516] [3517]
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
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[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3518] [3519]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3520]
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[]\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter,
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.1308 ...erapy for Stage B/C colon cancer}{colon}
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[] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[]
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[] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[]
[3522] [3523] [3524]
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[] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3525] [3526] [3527] [3528] [3529]
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[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
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\T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T
1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe-
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\T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv
(time, status) ~ age +
[3530]
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[][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][]
[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\
T1/ptm/m/n/10 ,
[3531]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3532] [3533] [3534] [3535] [3536] [3537] [3538] [3539]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
[3540]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3541] [3542] [3543]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3544] [3545] [3546]
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[3548]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3549]
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[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
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[]\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
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[] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[]
[3550] [3551]
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[] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3552] [3553]
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[] []
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[3555]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3556] [3557] [3558] [3559] [3560] [3561] [3562]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4210--4210
[] \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 )))[]
[3563] [3564]
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[]\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[]
[3565]
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[]\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[]
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[]\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2:
4] - yhat[1][]
[3566] [3567]
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[3569] [3570] [3571]
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[] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[]
[3572] [3573] [3574]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3575] [3576]
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[]\T1/pcr/m/n/9 mresid <- (lung$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[]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3577]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3578]
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[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[]
[3579]
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[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt
m/m/n/10 , which is the re-sult of the
[3580] [3581] [3582]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5512--5512
[]\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1
=FALSE, ...)
[3583]
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[]\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2
), se.fit=TRUE)[]
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[]\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval
ues smooth it.[]
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[]\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g
., svyglm, but[]
[3584]
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[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
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[] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[]
[3585] [3586]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3587]
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[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
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[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
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[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3588] [3589] [3590] [3591] [3592] [3593] [3594]
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[] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[]
[3595] [3596] [3597]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
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[]\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp
"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and
[3598] [3599] [3600] [3601] [3602]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[]
[3603] [3604]
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[]\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE)
[3605]
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[]\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem
ove duplicate times[]
[3606]
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[]\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times=
365*c(3, 5))[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.7224 ...ata from a soldering experiment}{solder}
[3607]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3608] [3609] [3610] [3611] [3612] [3613]
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[]\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[]
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[]\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[]
[3614] [3615] [3616] [3617]
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[] \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 ),[]
[3618] [3619] [3620] [3621]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods
first con-struct a sur-vival curve us-ing
[3622] [3623]
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[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3624] [3625] [3626]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
[3627]
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[]\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre
-dicted sur-vival
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3628]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3629] [3630] [3631] [3632]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10
,
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[] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
ctype,[]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
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[] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2
, ctype,[]
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[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
[3633] [3634] [3635]
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[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3636]
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\T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a-
lent to []\T1/pcr/m/n/10 stype=2,
[3637] [3638]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3639] [3640] [3641] [3642] [3643]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3644]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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[]\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) #
use concordance
[3645] [3646] [3647]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su
rvreg.distributions[][][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T
1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p
tm/m/n/10 ,
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[]\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, i
t is
[3648]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3649]
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[3650] [3651]
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[] \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 )[]
[3652]
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[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
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[] \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 )[]
[3653] [3654] [3655]
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[]\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100
0, data=test)[]
[3656] [3657]
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[]\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[]
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[]\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
set has data[]
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[] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[]
[3658] [3659] [3660] [3661] [3662] [3663] [3664]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3665] [3666] [3667]) [3668] (./fullrefman.ind [3669] [3670] [3671] [3672]
[3673] [3674] [3675] [3676] [3677] [3678] [3679] [3680] [3681] [3682] [3683]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
[3694] [3695] [3696] [3697] [3698] [3699]
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
[3700] [3701]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
[3702] [3703] [3704] [3705] [3706] [3707] [3708] [3709]
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[3710]
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[]\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method
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[]\T1/pcr/m/n/10 norm,denseMatrix,character-method
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[]\T1/pcr/m/n/10 norm,sparseMatrix,character-method
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[]\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method
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[]\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method
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[]\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method
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[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method
[3803]
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[]\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method
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[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method
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[3804]
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[]\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method
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[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,dgeMatrix,character-method
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[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method
[3806] [3807] [3808] [3809] [3810]
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method
[3811] [3812]
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[]\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method
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[]\T1/pcr/m/n/10 show,refClassRepresentation-method
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[]\T1/pcr/m/n/10 solve,CHMfactor,denseMatrix-method
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[]\T1/pcr/m/n/10 solve,CHMfactor,sparseMatrix-method
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[]\T1/pcr/m/n/10 solve,dtCMatrix,sparseMatrix-method
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[]\T1/pcr/m/n/10 solve,Matrix,sparseVector-method
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[]\T1/pcr/m/n/10 solve,matrix,sparseVector-method
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,sparseVector-method
[3817]
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[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_results
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[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings
[3819] [3820] [3821] [3822] [3823]
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[]\T1/pcr/m/n/10 tcrossprod,ANY,RsparseMatrix-method
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[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method
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mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/make
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/Rd
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/Rd/macros
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bib
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bst
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/tex/latex
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/bin
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make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl'
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make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/lib64/R"' \
-o Rscript ./Rscript.c
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/pkgconfig
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/exec
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/library
installing packages ...
building HTML index ...
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make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[1]: Nothing to be done for 'install'.
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/info
/usr/libexec/rpm-build/install -p -m 644 "./dir" "/usr/src/tmp/R-base-buildroot/usr/share/info"
installing R info pages ...
updating '/usr/share/info/dir' ...
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual'
make: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2'
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so
++ relative /usr/lib64/libR.so /usr/lib64/R/lib/libR.so
+ ln -s ../../libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so
+ ln -s libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR-2.11.so
++ relative /usr/share/doc/R-4.2 /usr/lib64/R/doc
+ ln -s ../../share/doc/R-4.2 /usr/src/tmp/R-base-buildroot/usr/lib64/R/doc
++ relative /usr/include/R /usr/lib64/R/include
+ ln -s ../../include/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/include
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/R
++ relative /usr/lib64/R/bin/R /usr/bin/R
+ ln -snfv ../lib64/R/bin/R /usr/src/tmp/R-base-buildroot/usr/bin/R
'/usr/src/tmp/R-base-buildroot/usr/bin/R' -> '../lib64/R/bin/R'
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/Rscript
++ relative /usr/lib64/R/bin/Rscript /usr/bin/Rscript
+ ln -snfv ../lib64/R/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/bin/Rscript
'/usr/src/tmp/R-base-buildroot/usr/bin/Rscript' -> '../lib64/R/bin/Rscript'
+ fgrep -r /usr/src/tmp/R-base-buildroot /usr/src/tmp/R-base-buildroot
fgrep: warning: fgrep is obsolescent; using grep -F
+ mkdir -p /usr/src/tmp/R-base-buildroot/etc/R
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Makeconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Renviron /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/javaconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/ldpaths /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/repositories /usr/src/tmp/R-base-buildroot/etc/R/
+ rmdir /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
++ relative /etc/R /usr/lib64/R/etc
+ ln -s ../../../etc/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
+ mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/applications
+ cat
+ '[' -f /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool ']'
++ relative /usr/bin/libtool /usr/lib64/R/bin/libtool
+ ln -snfv ../../../bin/libtool /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool
'/usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool' -> '../../../bin/libtool'
+ rm -fv /usr/src/tmp/R-base-buildroot/usr/share/info/dir
removed '/usr/src/tmp/R-base-buildroot/usr/share/info/dir'
+ /usr/lib/rpm/brp-alt
Cleaning files in /usr/src/tmp/R-base-buildroot (auto)
mode of './usr/lib64/libR.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/survival/libs/survival.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/mgcv/libs/mgcv.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/Matrix/libs/Matrix.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nlme/libs/nlme.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/rpart/libs/rpart.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/lattice/libs/lattice.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/spatial/libs/spatial.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nnet/libs/nnet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/KernSmooth/libs/KernSmooth.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/parallel/libs/parallel.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tcltk/libs/tcltk.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/splines/libs/splines.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grid/libs/grid.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/methods/libs/methods.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/stats/libs/stats.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/graphics/libs/graphics.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/cairo.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/grDevices.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/utils/libs/utils.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tools/libs/tools.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/R_de.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './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,gnuconfig)
/usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -fopenmp -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -fopenmp -L${rlibdir} -lR'
Checking contents of files in /usr/src/tmp/R-base-buildroot/ (default)
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: (from <cmdline>:0)
libR.so -> libR.so
./usr/lib64/R/lib: (from <cmdline>:0)
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)
Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.49583
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-4.2.2
+ export TZ=UTC
+ TZ=UTC
+ make check
make: Entering directory '/usr/src/RPM/BUILD/R-4.2.2'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/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
7432,7433c7432,7433
< Fisher's Exact Test for Count Data hybrid using asym.chisq. iff
< (exp=5, perc=80, Emin=1)
---
> Fisher's Exact Test for Count Data hybrid using asym.chisq. iff (exp=5,
> perc=80, Emin=1)
14066,14067c14066
< 4-sample test for equality of proportions without continuity
< correction
---
> 4-sample test for equality of proportions without continuity correction
14096,14097c14095
< 4-sample test for equality of proportions without continuity
< correction
---
> 4-sample test for equality of proportions without continuity correction
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-4.2.2/tests/Examples'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
running strict specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/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 'structure.R' ... OK
comparing 'structure.Rout' to './structure.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-4.2.2/tests'
running sloppy specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/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
running code in 'eval-etc-2.R' ... OK
comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
checking Sys.timezone ...
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
running code in 'timezone.R' ... OK
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
running regression tests ...
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/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 'd-p-q-r-tst-2.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-4.2.2/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/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' ... 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-4.2.2/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
running tests of Internet functions
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
running code in 'internet.R' ... OK
comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,145
< 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] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">"
> [2] "<html>"
> [3] "<head>"
> [4] "<title>The Comprehensive R Archive Network</title>"
> [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">"
> [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">"
> [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">"
> [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"
> [9] "</head>"
> [10] ""
> [11] "<FRAMESET cols=\"1*, 4*\" style=\"border: none;\">"
> [12] "<FRAMESET rows=\"120, 1*\">"
> [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"
> [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"
> [15] "</FRAMESET>"
> [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>"
> [17] "<noframes>"
> [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] "</noframes>"
> [23] "</FRAMESET>"
> > close(zz)
> >
> > # and via read.table
> >
> > 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
> >
OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests'
make: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2'
+ exit 0
Processing files: R-base-4.2.2-alt1
Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.7267
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-4.2.2
+ DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2
+ export DOCDIR
+ rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2
+ /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2
+ cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2
+ chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2
+ chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2
+ exit 0
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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/readRegistry.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/setWindowTitle.html
warning: File listed twice: /usr/lib64/R/library/utils/html/shortPathName.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/warnErrList.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winDialog.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winMenus.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winProgressBar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winextras.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.w1pX6J
find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,python3,shell,tcl,typelib)
lib.prov: /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so: 1310 symbols, 21 bpp
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
--- find-provides-deps 2023-09-02 02:08:51.851408103 +0000
+++ filter-provides-deps 2023-09-02 02:08:51.852408115 +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.ZqBnoI
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,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
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:jimQ7, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426DMNK4LZg18DsceiJLiUfETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQGxRy5H9jhHeHgWMWS5vZ9CCJh0Wm5, 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_2.17)(64bit), libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.27)(64bit), libc.so.6(GLIBC_2.3)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.33)(64bit), libc.so.6(GLIBC_2.34)(64bit), libc.so.6(GLIBC_2.38)(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:mfatAp2k43cHoHyudZ8yZim3OyQ01LIRoFeOerN9z5dbCyoZwgA6F1OPk550Z3ZCDOhgddN5H8RLBZo0M07mx3s6um9PpkKfPP9Nv0kAHUdUab4K3OOhNY9FTE18Xne0zzA8T8iZ4ZnO5SGudBdEgBn7o7QA0ppQr8ZbSfBHsIYjmCwbO0dKIPFkZJzK7PIj, libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, libgobject-2.0.so.0()(64bit) >= set:ml6W90, libgomp.so.1()(64bit) >= set:miW8hXcS41e0enAGr8Hj0enR52ADodkQIHD4LVrXNkg0, libgomp.so.1(GOMP_1.0)(64bit), libgomp.so.1(GOMP_4.0)(64bit), libgomp.so.1(GOMP_4.5)(64bit), libgomp.so.1(OMP_1.0)(64bit), libicui18n.so.73()(64bit) >= set:roSepFX4A5DMkWs1RT2X2vcia, libicuuc.so.73()(64bit) >= set:pmZb4GGICZzxKPlY0, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQITAzwZi7uccv48L3hfJPwCDlCRTQN0du6Hxf1PiwlB1IsJfGzE7kPRWTAeHIPYhIl5WiNVlN8FgR6mScaXXLmW0FDbvWuDSCea0aj0BvFxRc15QVQjV9n85Kyco0a0SzG6SwK1cfwAyHaix50g7p00c0WMF2, 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), libm.so.6(GLIBC_2.29)(64bit), libm.so.6(GLIBC_2.35)(64bit), libm.so.6(GLIBC_2.38)(64bit), libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQCfq9fPhNQgw41BExdcI9mdt, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgdZcM1, libpcre2-8.so.0()(64bit) >= set:kfq9tJAJZakapZcr8gHlRiHX2PuBva483hqVseVZw6HMZF1, libpng16.so.16()(64bit) >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng16.so.16(PNG16_0)(64bit), libreadline.so.7()(64bit) >= set:nidQ8PMktsCwid18OsyEUS8iDQRn5631GOVow7aaRTmMg1UZho7I5k7dG1ZFel4iyBQZd1aPRdDv8sK6EUfgoB1, 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.kNXQI0
Creating R-base-debuginfo package
Processing files: R-full-4.2.2-alt1
Requires: R-devel = 4.2.2-alt1, R-tcltk = 4.2.2-alt1, R-doc-html = 4.2.2-alt1, gcc-c++, gcc-fortran, liblapack-devel, make
Processing files: R-devel-4.2.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.gBDxVR
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,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.ANVHWy
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,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
43 | # 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
43 | # 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 rmdir
Provides: pkgconfig(libR) = 4.2.2
Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils
Requires(pre): R-base = 4.2.2-alt1
Requires(postun): R-base = 4.2.2-alt1
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.nKdqkR
Processing files: R-tcltk-4.2.2-alt1
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.VSUnzn
find-provides: running scripts (alternatives,debuginfo,gir,lib,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.Ti6D1j
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Provides: tcl(::Utility), tcl(::Utility)-1 = 1.0, tcl(::Utility::dump), tcl(::Utility::dump)-1 = 1.0, tcl(::Utility::expand), tcl(::Utility::expand)-1 = 1.0, tcl(::Utility::number), tcl(::Utility::number)-1 = 1.0, tcl(::Utility::string), tcl(::Utility::string)-1 = 1.0, tcl(::Utility::tk), tcl(::Utility::tk)-1 = 1.0, tcl(Hierarchy), tcl(Hierarchy)-2 = 2.0, tcl(PBar), tcl(PBar)-1 = 1.0, tcl(Widget), tcl(Widget)-2 = 2.0
Requires: R-base = 4.2.2-alt1, libR.so()(64bit) >= set:oiZ4ZDvavdS7yJmmEm1yk76RAJNZigoIdZ4rGSanE1atzKMNmL5wj1XTzOOW0cQ6tLN8BjJrkKZnL1TEzhiItObZCaSl9pqVwPzwTv35ZmWMAXnz5WOfaBOCf02nKkV441OH5pR09Da07HhWgbjgmeagfNIHgS1oluZiX23S3, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.38)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.6.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.6.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk), tcl(Tk)-8 >= 8
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.qrmLdv
Creating R-tcltk-debuginfo package
Processing files: R-doc-html-4.2.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.0uOO2J
find-provides: running scripts (alternatives,debuginfo,gir,lib,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.zph8Vv
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Requires: R-base = 4.2.2-alt1, xdg-utils
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.7xE30I
Processing files: R-doc-pdf-4.2.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.mKFLvt
find-provides: running scripts (alternatives,debuginfo,gir,lib,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.AvLaHU
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Requires: xdg-utils
Conflicts: R-base > 4.2.2, R-base < 4.2.2
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.QAHjxB
Processing files: R-doc-info-4.2.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.WK6fQ1
find-provides: running scripts (alternatives,debuginfo,gir,lib,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.Z8rSOt
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Conflicts: R-base > 4.2.2, R-base < 4.2.2
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.NF6soP
Processing files: R-base-debuginfo-4.2.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ZPPCDy
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.ZZL7sz
find-requires: running scripts (debuginfo)
Provides: debug64(libR.so)
Requires: R-base = 4.2.2-alt1, /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(libgobject-2.0.so.0), debug64(libgomp.so.1), debug64(libicui18n.so.73), debug64(libicuuc.so.73), 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(libpcre2-8.so.0), debug64(libpng16.so.16), debug64(libreadline.so.7), debug64(libtiff.so.5), debug64(libz.so.1)
Processing files: R-tcltk-debuginfo-4.2.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.0xjkn2
find-provides: running scripts (debuginfo)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.qiwK6W
find-requires: running scripts (debuginfo)
Requires: R-tcltk = 4.2.2-alt1, debug64(libR.so), debug64(libc.so.6), debug64(libtcl8.6.so), debug64(libtk8.6.so)
Adding to R-devel a strict dependency on R-base
Adding to R-tcltk a strict dependency on R-base
Adding to R-doc-html a strict dependency on R-base
Adding to R-base-debuginfo a strict dependency on R-base
Adding to R-full a strict dependency on R-devel
Adding to R-full a strict dependency on R-tcltk
Adding to R-full a strict dependency on R-doc-html
Adding to R-tcltk-debuginfo a strict dependency on R-tcltk
Adding to R-devel a strict dependency on R-base
Adding to R-tcltk-debuginfo a strict dependency on R-base-debuginfo
Removing from R-tcltk-debuginfo 12 sources provided by R-base-debuginfo
also prunning dir /usr/src/debug/R-4.2.2/include/R_ext
also prunning dir /usr/src/debug/R-4.2.2/src/include
also prunning dir /usr/src/debug/R-4.2.2/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 6 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
Wrote: /usr/src/RPM/RPMS/x86_64/R-base-4.2.2-alt1.x86_64.rpm (w2T16.xzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-full-4.2.2-alt1.x86_64.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-4.2.2-alt1.x86_64.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-4.2.2-alt1.x86_64.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-doc-html-4.2.2-alt1.x86_64.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-doc-pdf-4.2.2-alt1.x86_64.rpm (w2T16.xzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-doc-info-4.2.2-alt1.x86_64.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-4.2.2-alt1.x86_64.rpm (w2T16.xzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-4.2.2-alt1.x86_64.rpm (w2.lzdio)
755.01user 180.18system 7:51.93elapsed 198%CPU (0avgtext+0avgdata 697240maxresident)k
0inputs+0outputs (0major+22936402minor)pagefaults 0swaps
6.95user 3.66system 10:11.91elapsed 1%CPU (0avgtext+0avgdata 131336maxresident)k
3730032inputs+0outputs (0major+343816minor)pagefaults 0swaps
--- R-base-4.2.2-alt1.x86_64.rpm.repo 2023-07-27 12:28:09.000000000 +0000
+++ R-base-4.2.2-alt1.x86_64.rpm.hasher 2023-09-02 02:09:49.319067257 +0000
@@ -13212,2 +13212,3 @@
Requires: libc.so.6(GLIBC_2.34)(64bit)
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Requires: libc.so.6(GLIBC_2.4)(64bit)
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Requires: libm.so.6(GLIBC_2.35)(64bit)
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Requires: libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02
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