<86>Aug 7 01:42:16 userdel[220864]: delete user 'rooter'
<86>Aug 7 01:42:16 userdel[220864]: removed group 'rooter' owned by 'rooter'
<86>Aug 7 01:42:16 userdel[220864]: removed shadow group 'rooter' owned by 'rooter'
<86>Aug 7 01:42:16 groupadd[220877]: group added to /etc/group: name=rooter, GID=525
<86>Aug 7 01:42:16 groupadd[220877]: group added to /etc/gshadow: name=rooter
<86>Aug 7 01:42:16 groupadd[220877]: new group: name=rooter, GID=525
<86>Aug 7 01:42:16 useradd[220888]: new user: name=rooter, UID=525, GID=525, home=/root, shell=/bin/bash
<86>Aug 7 01:42:16 userdel[220898]: delete user 'builder'
<86>Aug 7 01:42:16 userdel[220898]: removed group 'builder' owned by 'builder'
<86>Aug 7 01:42:16 userdel[220898]: removed shadow group 'builder' owned by 'builder'
<86>Aug 7 01:42:16 groupadd[220907]: group added to /etc/group: name=builder, GID=526
<86>Aug 7 01:42:16 groupadd[220907]: group added to /etc/gshadow: name=builder
<86>Aug 7 01:42:16 groupadd[220907]: new group: name=builder, GID=526
<86>Aug 7 01:42:16 useradd[220914]: new user: name=builder, UID=526, GID=526, home=/usr/src, shell=/bin/bash
warning: Macro %add_tcl_lib_path not found
<13>Aug 7 01:42:27 rpmi: libpng16-1.6.37-alt1 sisyphus+236677.100.2.1 1566917982 installed
<13>Aug 7 01:42:27 rpmi: xorg-proto-devel-2020.1-alt1 sisyphus+250406.100.1.1 1587554810 installed
<13>Aug 7 01:42:27 rpmi: libjpeg-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed
<13>Aug 7 01:42:27 rpmi: libexpat-2.2.9-alt1 sisyphus+252464.200.2.1 1590958863 installed
<13>Aug 7 01:42:27 rpmi: python-base-2.7.17-alt3 sisyphus+240580.60.5.1 1573516903 installed
<13>Aug 7 01:42:27 rpmi: libglvnd-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124262 installed
<13>Aug 7 01:42:27 rpmi: perl-HTTP-Date-6.04-alt1 sisyphus+241046.100.1.1 1574192946 installed
<13>Aug 7 01:42:27 rpmi: libICE-1.0.10-alt1 sisyphus+247690.100.1.1 1584000383 installed
<13>Aug 7 01:42:27 rpmi: libSM-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed
<13>Aug 7 01:42:27 rpmi: tex-common-0.2-alt4 1244804096 installed
<13>Aug 7 01:42:27 rpmi: libopenblas-0.3.9-alt1 sisyphus+238855.200.5.1 1593950265 installed
<13>Aug 7 01:42:27 rpmi: perl-Unicode-Normalize-1:5.28.2-alt3 sisyphus+246858.100.1.1 1582561863 installed
<13>Aug 7 01:42:27 rpmi: perl-Term-ANSIColor-5.01-alt1 sisyphus+244783.100.1.2 1579747505 installed
<13>Aug 7 01:42:27 rpmi: libpaper-1.1.26-alt1 sisyphus+221360.100.1.1 1549974198 installed
<13>Aug 7 01:42:28 rpmi: libicu67-1:6.7.1-alt2 sisyphus+252432.100.2.2 1590796031 installed
<13>Aug 7 01:42:28 rpmi: libgraphite2-1.3.14-alt2 sisyphus+250009.100.1.1 1586943071 installed
<13>Aug 7 01:42:28 rpmi: libgdbm-1.8.3-alt10 1454943313 installed
<13>Aug 7 01:42:28 rpmi: psutils-2:1.23-alt2 sisyphus+226711.100.1.1 1554520810 installed
<13>Aug 7 01:42:28 rpmi: libjasper-2.0.16-alt1 sisyphus+231386.100.1.1 1559568071 installed
<13>Aug 7 01:42:28 rpmi: rpm-macros-info-install-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Aug 7 01:42:28 rpmi: zlib-devel-1.2.11-alt1 sisyphus+221902.6000.4.1 1550600768 installed
<13>Aug 7 01:42:28 rpmi: liblksctp-1.0.17-alt2 1523113258 installed
<13>Aug 7 01:42:28 rpmi: libnspr-1:4.27-alt1 sisyphus+255566.100.1.1 1596128006 installed
<13>Aug 7 01:42:28 rpmi: libidn2-2.3.0-alt1 sisyphus+240846.100.1.2 1573870464 installed
<13>Aug 7 01:42:28 rpmi: libpixman-3:0.40.0-alt1 sisyphus+250700.100.1.1 1587970807 installed
<13>Aug 7 01:42:28 rpmi: libwayland-server-1.18.0-alt1 sisyphus+255795.100.1.1 1596475645 installed
<13>Aug 7 01:42:28 rpmi: libtcl-8.6.10-alt1 sisyphus+241485.100.1.1 1574408296 installed
<13>Aug 7 01:42:28 rpmi: tcl-8.6.10-alt1 sisyphus+241485.100.1.1 1574408296 installed
<13>Aug 7 01:42:28 rpmi: libsqlite3-3.32.3-alt1 sisyphus+253798.100.1.1 1592756027 installed
<13>Aug 7 01:42:28 rpmi: python-module-sphinxcontrib-2.1.1-alt2.1.2 sisyphus+227529.1100.1.2 1555924423 installed
<13>Aug 7 01:42:29 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed
<13>Aug 7 01:42:29 rpmi: perl-IO-stringy-2.111-alt1 1432302202 installed
<13>Aug 7 01:42:29 rpmi: perl-Tie-RefHash-1.39-alt1 1316492563 installed
<13>Aug 7 01:42:29 rpmi: perl-IO-Socket-IP-0.39-alt1 1494508514 installed
<13>Aug 7 01:42:29 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed
<13>Aug 7 01:42:29 rpmi: perl-Compress-Raw-Zlib-2.095-alt1 sisyphus+255277.100.1.1 1595512157 installed
<13>Aug 7 01:42:29 rpmi: perl-libnet-1:3.11-alt1 1511423541 installed
<13>Aug 7 01:42:29 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed
<13>Aug 7 01:42:29 rpmi: libXau-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed
<13>Aug 7 01:42:29 rpmi: libwebp7-1.1.0-alt1 sisyphus+243895.100.1.1 1578410876 installed
<13>Aug 7 01:42:29 rpmi: libjbig-2.1-alt1 1401380921 installed
<13>Aug 7 01:42:29 rpmi: libtiff5-4.1.0-alt1 sisyphus+240802.100.1.1 1573743630 installed
<13>Aug 7 01:42:29 rpmi: libopenjpeg2.0-2.3.1-alt1 sisyphus+226454.100.1.1 1554284336 installed
<13>Aug 7 01:42:29 rpmi: libquadmath0-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:29 rpmi: libgfortran5-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:29 rpmi: libquadmath9-devel-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:29 rpmi: libXau-devel-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed
<13>Aug 7 01:42:29 rpmi: perl-autodie-2.32-alt1 sisyphus+244764.100.1.1 1579724522 installed
<13>Aug 7 01:42:29 rpmi: perl-OLE-Storage_Lite-0.20-alt1 sisyphus+243912.100.1.1 1578493389 installed
<13>Aug 7 01:42:29 rpmi: lksctp-tools-1.0.17-alt2 1523113258 installed
<13>Aug 7 01:42:29 rpmi: libpng-devel-1.6.37-alt1 sisyphus+236677.100.2.1 1566917982 installed
<13>Aug 7 01:42:29 rpmi: libgdbm-devel-1.8.3-alt10 1454943313 installed
<13>Aug 7 01:42:29 rpmi: libgraphite2-devel-1.3.14-alt2 sisyphus+250009.100.1.1 1586943071 installed
<13>Aug 7 01:42:29 rpmi: icu-utils-1:6.7.1-alt2 sisyphus+252432.100.2.2 1590796031 installed
<13>Aug 7 01:42:29 rpmi: libicu-devel-1:6.7.1-alt2 sisyphus+252432.100.2.2 1590796031 installed
<13>Aug 7 01:42:29 rpmi: perl-Data-Dump-1.23-alt1 1444601978 installed
<13>Aug 7 01:42:29 rpmi: perl-unicore-1:5.28.2-alt3 sisyphus+246858.100.1.1 1582561863 installed
<13>Aug 7 01:42:29 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+221481.100.1.1 1550127189 installed
<13>Aug 7 01:42:29 rpmi: libopenblas-devel-0.3.9-alt1 sisyphus+238855.200.5.1 1593950265 installed
<13>Aug 7 01:42:29 rpmi: libICE-devel-1.0.10-alt1 sisyphus+247690.100.1.1 1584000383 installed
<13>Aug 7 01:42:29 rpmi: libSM-devel-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed
<13>Aug 7 01:42:29 rpmi: perl-File-Listing-6.04-alt1 1329758996 installed
<13>Aug 7 01:42:29 rpmi: libOpenGL-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124262 installed
<13>Aug 7 01:42:29 rpmi: libGLES-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124262 installed
<13>Aug 7 01:42:29 rpmi: python-module-imagesize-1.1.0-alt1 sisyphus+229015.100.2.1 1557233756 installed
<13>Aug 7 01:42:29 rpmi: python-module-apipkg-1.5-alt1 1531926894 installed
<13>Aug 7 01:42:29 rpmi: rpm-build-tcl-0.5.2-alt1 sisyphus+248358.100.2.1 1585272688 installed
<13>Aug 7 01:42:29 rpmi: tcl-devel-8.6.10-alt1 sisyphus+241485.100.1.1 1574408296 installed
<13>Aug 7 01:42:29 rpmi: rpm-macros-java-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed
<13>Aug 7 01:42:29 rpmi: perl-Algorithm-Diff-1.1903-alt1 1418755800 installed
<13>Aug 7 01:42:29 rpmi: perl-Unicode-EastAsianWidth-12.0-alt1 sisyphus+237401.100.1.1 1568197363 installed
<13>Aug 7 01:42:29 rpmi: lua5.3-5.3.5-alt3 sisyphus+237725.540.7.3 1569407850 installed
<13>Aug 7 01:42:29 rpmi: libtre5-0.8.0-alt2.2 sisyphus+249319.100.1.1 1585933005 installed
<13>Aug 7 01:42:29 rpmi: libpcre2-10.35-alt1 sisyphus+251510.100.1.1 1589115548 installed
<13>Aug 7 01:42:29 rpmi: libgomp1-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:29 rpmi: libpcsclite-1.9.0-alt1 sisyphus+253463.100.1.1 1592202073 installed
<13>Aug 7 01:42:29 rpmi: javazi-2020a-alt1 sisyphus+250575.200.1.1 1587740494 installed
<13>Aug 7 01:42:29 rpmi: javapackages-filesystem-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed
<13>Aug 7 01:42:29 rpmi: javapackages-tools-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed
<13>Aug 7 01:42:29 rpmi: java-common-1.6.0-alt1 sisyphus+234020.100.1.1 1562437039 installed
<13>Aug 7 01:42:29 rpmi: libgif-4.1.6-alt3 1299634266 installed
<13>Aug 7 01:42:30 rpmi: libgtk+2-locales-2.24.32-alt4 sisyphus+248211.200.2.1 1584869557 installed
<13>Aug 7 01:42:30 rpmi: libdatrie-0.2.9-alt1_6 1511686677 installed
<13>Aug 7 01:42:30 rpmi: libthai-0.1.28-alt1_1 sisyphus+226107.100.1.1 1554123079 installed
<13>Aug 7 01:42:30 rpmi: libfribidi-1.0.10-alt1 sisyphus+254557.100.1.1 1594020354 installed
<13>Aug 7 01:42:30 rpmi: libatk-locales-2.36.0-alt1 sisyphus+249208.100.1.1 1585840405 installed
<13>Aug 7 01:42:30 rpmi: libatk-2.36.0-alt1 sisyphus+249208.100.1.1 1585840405 installed
<13>Aug 7 01:42:30 rpmi: icon-theme-hicolor-0.17-alt2 sisyphus+248343.100.1.1 1584979043 installed
<13>Aug 7 01:42:30 rpmi: shared-mime-info-2.0-alt1 sisyphus+251302.100.1.1 1588847587 installed
<13>Aug 7 01:42:30 rpmi: libgdk-pixbuf-locales-2.40.0-alt1 sisyphus+238952.140.2.1 1570644607 installed
<13>Aug 7 01:42:30 rpmi: gsettings-desktop-schemas-data-3.36.1-alt1 sisyphus+250870.100.1.1 1588227108 installed
<13>Aug 7 01:42:30 rpmi: libgio-2.64.4-alt1 sisyphus+254365.100.1.1 1593701005 installed
<13>Aug 7 01:42:30 rpmi: gsettings-desktop-schemas-3.36.1-alt1 sisyphus+250870.100.1.1 1588227108 installed
<13>Aug 7 01:42:30 rpmi: libgdk-pixbuf-2.40.0-alt1 sisyphus+238952.140.2.1 1570644607 installed
<13>Aug 7 01:42:30 rpmi: gtk-update-icon-cache-3.24.21-alt1 sisyphus+254255.100.1.1 1593514263 installed
<13>Aug 7 01:42:30 rpmi: libkpathsea6-2019-alt1_7 sisyphus+255755.100.1.1 1596460832 installed
<13>Aug 7 01:42:30 rpmi: libptexenc1-2019-alt1_7 sisyphus+255755.100.1.1 1596460832 installed
<13>Aug 7 01:42:30 rpmi: libsynctex2-2019-alt1_7 sisyphus+255755.100.1.1 1596460832 installed
<13>Aug 7 01:42:30 rpmi: libtexlua5-2019-alt1_7 sisyphus+255755.100.1.1 1596460832 installed
<13>Aug 7 01:42:30 rpmi: zziplib-0.13.69-alt3 sisyphus+240928.100.1.1 1574074941 installed
<13>Aug 7 01:42:30 rpmi: liblcms2-2.11-alt1 sisyphus+253499.100.1.1 1592286997 installed
<13>Aug 7 01:42:30 rpmi: publicsuffix-list-dafsa-20200720-alt1 sisyphus+255208.100.1.1 1595349910 installed
<13>Aug 7 01:42:30 rpmi: libpsl-0.21.1-alt1 sisyphus+255206.100.1.1 1595348931 installed
<13>Aug 7 01:42:30 rpmi: libnghttp2-1.41.0-alt1 sisyphus+253680.100.1.1 1592642263 installed
<13>Aug 7 01:42:30 rpmi: poppler-data-0.4.9-alt1 sisyphus.216033.100 1541141723 installed
<13>Aug 7 01:42:30 rpmi: libxshmfence-1.3-alt1 sisyphus+223149.1000.2.1 1551268594 installed
<13>Aug 7 01:42:30 rpmi: libwayland-client-1.18.0-alt1 sisyphus+255795.100.1.1 1596475645 installed
<13>Aug 7 01:42:30 rpmi: libpciaccess-1:0.16-alt1 sisyphus+234814.100.1.1 1563438297 installed
<13>Aug 7 01:42:30 rpmi: libdrm-1:2.4.102-alt1 sisyphus+252307.100.1.1 1590574831 installed
<13>Aug 7 01:42:30 rpmi: libgbm-4:20.1.4-alt1 sisyphus+255250.100.1.1 1595485574 installed
<13>Aug 7 01:42:30 rpmi: t1utils-1.41-alt1 1502978415 installed
<13>Aug 7 01:42:30 rpmi: libqqwing-1.3.4-alt2 1436192940 installed
<13>Aug 7 01:42:30 rpmi: qqwing-1.3.4-alt2 1436192940 installed
<13>Aug 7 01:42:30 rpmi: python-module-iniconfig-1.0.0-alt2 sisyphus+235493.2400.6.1 1565442448 installed
<13>Aug 7 01:42:30 rpmi: python-sphinx-objects.inv-1:2.3.10.20200721-alt1 sisyphus+255227.100.1.1 1595375747 installed
<13>Aug 7 01:42:31 rpmi: libxapian-1.4.15-alt1 sisyphus+248304.20.4.1 1585071487 installed
<13>Aug 7 01:42:31 rpmi: python-module-google-0.4.2-alt2.1 sisyphus+228356.1500.3.1 1556633038 installed
<13>Aug 7 01:42:31 rpmi: python-module-markupsafe-1.1.1-alt1 sisyphus+248369.100.1.1 1585046156 installed
<13>Aug 7 01:42:31 rpmi: python-module-enum34-1.1.6-alt3 1527251693 installed
<13>Aug 7 01:42:31 rpmi: libnumpy-1:1.15.4-alt5 sisyphus+247694.100.3.3 1584382457 installed
<13>Aug 7 01:42:31 rpmi: libxblas-1.0.248-alt1.3 sisyphus+229150.100.1.1 1557388758 installed
<13>Aug 7 01:42:31 rpmi: liblapack-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed
<13>Aug 7 01:42:31 rpmi: python-modules-curses-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:31 rpmi: libverto-0.3.0-alt1_7 sisyphus+225932.100.1.1 1553994917 installed
<13>Aug 7 01:42:31 rpmi: liblmdb-0.9.23-alt1 sisyphus+225277.100.2.1 1553001689 installed
<13>Aug 7 01:42:31 rpmi: libkeyutils-1.6-alt2 sisyphus+226520.100.2.1 1554512088 installed
<13>Aug 7 01:42:31 rpmi: libcom_err-1.44.6-alt1 sisyphus+224154.100.1.1 1552091653 installed
<13>Aug 7 01:42:31 rpmi: perl-Unicode-Map-0.112-alt7.1 sisyphus+219907.5000.1.1 1548349925 installed
<13>Aug 7 01:42:31 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed
<13>Aug 7 01:42:31 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed
<13>Aug 7 01:42:31 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed
<13>Aug 7 01:42:31 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed
<13>Aug 7 01:42:31 rpmi: perl-IPC-System-Simple-1.30-alt1 sisyphus+248544.100.1.1 1585154078 installed
<13>Aug 7 01:42:31 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed
<13>Aug 7 01:42:31 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed
<13>Aug 7 01:42:31 rpmi: perl-File-Which-1.23-alt1 sisyphus.218871.100 1546337313 installed
<13>Aug 7 01:42:31 rpmi: perl-File-Copy-Recursive-0.45-alt1 sisyphus+235291.100.1.1 1564606222 installed
<13>Aug 7 01:42:31 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+219907.4500.1.1 1548349730 installed
<13>Aug 7 01:42:31 rpmi: perl-TimeDate-2.33-alt1 sisyphus+252901.100.1.1 1591387378 installed
<13>Aug 7 01:42:31 rpmi: less-530-alt1 sisyphus+226367.200.2.2 1554151813 installed
<13>Aug 7 01:42:31 rpmi: perl-Try-Tiny-0.30-alt1 1514318058 installed
<13>Aug 7 01:42:31 rpmi: perl-Compress-Raw-Bzip2-2.095-alt1 sisyphus+255276.100.1.1 1595511686 installed
<13>Aug 7 01:42:31 rpmi: libdb4.7-devel-4.7.25-alt9 1490438456 installed
<13>Aug 7 01:42:31 rpmi: perl-devel-1:5.28.2-alt3 sisyphus+246858.100.1.1 1582561863 installed
<13>Aug 7 01:42:31 rpmi: hd2u-1.0.3-alt2 1400842666 installed
<13>Aug 7 01:42:31 rpmi: perl-Filter-1.59-alt1.1 sisyphus+219907.400.1.1 1548343225 installed
<13>Aug 7 01:42:31 rpmi: perl-Encode-3.04-alt1 sisyphus+247835.100.1.1 1584190284 installed
<13>Aug 7 01:42:31 rpmi: perl-URI-1.76-alt1 sisyphus+220243.100.1.1 1548863244 installed
<13>Aug 7 01:42:31 rpmi: perl-HTML-Parser-3.72-alt1.2 sisyphus+219907.600.1.1 1548343407 installed
<13>Aug 7 01:42:31 rpmi: perl-IO-Compress-2.093-alt1 sisyphus+243543.100.1.1 1577294382 installed
<13>Aug 7 01:42:31 rpmi: perl-Net-HTTP-6.19-alt1 sisyphus+229756.100.1.1 1558454558 installed
<13>Aug 7 01:42:31 rpmi: perl-Pod-Simple-3.40-alt1 sisyphus+239861.100.1.1 1572267919 installed
<13>Aug 7 01:42:31 rpmi: perl-Pod-Usage-1.70-alt1 sisyphus+248549.100.1.1 1585154783 installed
<13>Aug 7 01:42:31 rpmi: perl-podlators-4.14-alt1 sisyphus+243914.100.1.1 1578493399 installed
<13>Aug 7 01:42:31 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed
<13>Aug 7 01:42:31 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed
<13>Aug 7 01:42:31 rpmi: perl-IO-HTML-1.001-alt1 1404821752 installed
<13>Aug 7 01:42:31 rpmi: perl-HTTP-Message-6.25-alt1 sisyphus+254521.100.1.1 1593894315 installed
<13>Aug 7 01:42:31 rpmi: perl-HTTP-Cookies-6.08-alt1 sisyphus+242242.100.1.1 1575454022 installed
<13>Aug 7 01:42:31 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed
<13>Aug 7 01:42:31 rpmi: perl-libwww-6.46-alt1 sisyphus+254012.100.1.1 1593105927 installed
<13>Aug 7 01:42:31 rpmi: perl-XML-Parser-2.44-alt2.2 sisyphus+219907.1300.1.1 1548343654 installed
<13>Aug 7 01:42:31 rpmi: perl-HTML-Tree-5.07-alt1 1506480309 installed
<13>Aug 7 01:42:31 rpmi: perl-HTML-Formatter-2.16-alt1 1482105372 installed
<13>Aug 7 01:42:31 rpmi: perl-XML-XPath-1.44-alt1 sisyphus.215541.100 1540451758 installed
<13>Aug 7 01:42:31 rpmi: perl-HTML-Form-6.07-alt1 sisyphus+246847.100.1.1 1582555741 installed
<13>Aug 7 01:42:31 rpmi: perl-WWW-Mechanize-2.00-alt1 sisyphus+254025.100.1.2 1593124352 installed
<13>Aug 7 01:42:31 rpmi: perl-XML-Writer-0.625-alt1 1402417374 installed
<13>Aug 7 01:42:31 rpmi: hwinfo-utils-21.23-alt1.1 sisyphus+248432.200.2.1 1585065321 installed
<13>Aug 7 01:42:31 rpmi: perl-Text-CSV_XS-1.44-alt1 sisyphus+255292.100.1.1 1595514625 installed
<13>Aug 7 01:42:31 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed
<13>Aug 7 01:42:31 rpmi: perl-libintl-1.31-alt1.1 sisyphus+219907.6300.1.1 1548352427 installed
<13>Aug 7 01:42:32 rpmi: libteckit-2.5.1-alt2.1 1319227424 installed
<13>Aug 7 01:42:32 rpmi: libteckit-utils-2.5.1-alt2.1 1319227424 installed
<13>Aug 7 01:42:32 rpmi: rgb-1.0.6-alt3 sisyphus+229441.100.1.2 1557940332 installed
<13>Aug 7 01:42:32 rpmi: libnetpbm11-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed
<13>Aug 7 01:42:32 rpmi: mailx-8.1.2-alt7 1366314831 installed
<13>Aug 7 01:42:32 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed
<13>Aug 7 01:42:32 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed
<13>Aug 7 01:42:32 rpmi: libX11-locales-3:1.6.9-alt1 sisyphus+239210.100.1.1 1571056781 installed
<13>Aug 7 01:42:32 rpmi: libXdmcp-1.1.3-alt1 sisyphus+225206.600.1.2 1552949347 installed
<13>Aug 7 01:42:32 rpmi: libxcb-1.14-alt1 sisyphus+247358.200.1.3 1583854223 installed
<13>Aug 7 01:42:32 rpmi: libX11-3:1.6.9-alt1 sisyphus+239210.100.1.1 1571056781 installed
<13>Aug 7 01:42:32 rpmi: libXext-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed
<13>Aug 7 01:42:32 rpmi: libXrender-0.9.8-alt1 1371312110 installed
<13>Aug 7 01:42:32 rpmi: libXt-1.2.0-alt1 sisyphus+247690.400.1.1 1584000566 installed
<13>Aug 7 01:42:32 rpmi: libXmu-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed
<13>Aug 7 01:42:32 rpmi: libXfixes-5.0.3-alt1 sisyphus+226736.100.2.2 1554614842 installed
<13>Aug 7 01:42:32 rpmi: libXpm-3.5.13-alt1 sisyphus+247690.300.1.1 1584000502 installed
<13>Aug 7 01:42:32 rpmi: libXi-1.7.10-alt1 sisyphus+232786.300.1.1 1561106975 installed
<13>Aug 7 01:42:32 rpmi: libXdamage-1.1.5-alt1 sisyphus+225206.500.1.2 1552949282 installed
<13>Aug 7 01:42:32 rpmi: libXcomposite-0.4.5-alt1 sisyphus+225206.300.1.2 1552949136 installed
<13>Aug 7 01:42:34 rpmi: libxcb-devel-1.14-alt1 sisyphus+247358.200.1.3 1583854223 installed
<13>Aug 7 01:42:34 rpmi: libX11-devel-3:1.6.9-alt1 sisyphus+239210.100.1.1 1571056781 installed
<13>Aug 7 01:42:34 rpmi: libXrender-devel-0.9.8-alt1 1371312110 installed
<13>Aug 7 01:42:34 rpmi: libXext-devel-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed
<13>Aug 7 01:42:34 rpmi: libXt-devel-1.2.0-alt1 sisyphus+247690.400.1.1 1584000566 installed
<13>Aug 7 01:42:34 rpmi: libXaw-1.0.12-alt1 1391072621 installed
<13>Aug 7 01:42:34 rpmi: libXcursor-1.2.0-alt1 sisyphus+225206.400.1.2 1552949214 installed
<13>Aug 7 01:42:34 rpmi: xset-1.2.4-alt1 sisyphus.213358.100 1537438593 installed
<13>Aug 7 01:42:34 rpmi: libXrandr-1.5.2-alt1 sisyphus+225206.1300.1.2 1552949698 installed
<13>Aug 7 01:42:34 rpmi: libXxf86vm-1.1.4-alt2 1527672159 installed
<13>Aug 7 01:42:34 rpmi: libGLX-mesa-4:20.1.4-alt1 sisyphus+255250.100.1.1 1595485574 installed
<13>Aug 7 01:42:34 rpmi: libEGL-mesa-4:20.1.4-alt1 sisyphus+255250.100.1.1 1595485574 installed
<13>Aug 7 01:42:34 rpmi: libEGL-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124262 installed
<13>Aug 7 01:42:34 rpmi: libGLX-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124262 installed
<13>Aug 7 01:42:34 rpmi: libGL-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124262 installed
<13>Aug 7 01:42:34 rpmi: libglvnd-devel-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124262 installed
<13>Aug 7 01:42:34 rpmi: libEGL-devel-4:20.1.4-alt1 sisyphus+255250.100.1.1 1595485574 installed
<13>Aug 7 01:42:34 rpmi: libGL-devel-4:20.1.4-alt1 sisyphus+255250.100.1.1 1595485574 installed
<13>Aug 7 01:42:34 rpmi: libXinerama-1.1.4-alt1 sisyphus+223149.300.2.1 1551268223 installed
<13>Aug 7 01:42:34 rpmi: libXtst-1.2.2-alt1 1369984880 installed
<13>Aug 7 01:42:34 rpmi: netpbm-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed
<13>Aug 7 01:42:34 rpmi: xprop-1.2.4-alt1 sisyphus+225764.100.1.1 1553680701 installed
<13>Aug 7 01:42:34 rpmi: xdg-utils-1.1.3-alt6 sisyphus+233067.100.1.1 1561332512 installed
<13>Aug 7 01:42:34 rpmi: liblz4-1:1.9.2-alt1 sisyphus+238585.100.2.2 1570066861 installed
<13>Aug 7 01:42:34 rpmi: libgpg-error-1.36-alt1 sisyphus+225621.300.1.1 1553521088 installed
<13>Aug 7 01:42:34 rpmi: libgcrypt20-1.8.5-alt3 sisyphus+239622.100.1.1 1571746563 installed
<13>Aug 7 01:42:34 rpmi: libxslt-1.1.34-alt2 sisyphus+248264.100.1.1 1584829787 installed
<13>Aug 7 01:42:34 rpmi: libsystemd-1:246-alt1 sisyphus+255831.100.2.1 1596565305 installed
<13>Aug 7 01:42:34 rpmi: libdbus-1.12.18-alt1 sisyphus+252758.100.1.1 1591203684 installed
<13>Aug 7 01:42:34 rpmi: libavahi-0.8-alt1 sisyphus+255349.240.4.1 1595604500 installed
<13>Aug 7 01:42:34 rpmi: libcups-2.3.1-alt2 sisyphus+255816.100.2.1 1596533608 installed
<13>Aug 7 01:42:34 rpmi: gcc-fortran-common-1.4.25-alt1 sisyphus+255450.100.1.1 1595851517 installed
<13>Aug 7 01:42:34 rpmi: libgfortran9-devel-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:35 rpmi: gcc9-fortran-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:35 rpmi: gcc-c++-common-1.4.25-alt1 sisyphus+255450.100.1.1 1595851517 installed
<13>Aug 7 01:42:36 rpmi: libstdc++9-devel-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:37 rpmi: gcc9-c++-9.3.1-alt1 sisyphus+251917.40.3.1 1589811833 installed
<13>Aug 7 01:42:37 rpmi: libbrotlicommon-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed
<13>Aug 7 01:42:37 rpmi: libbrotlidec-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed
<13>Aug 7 01:42:37 rpmi: libharfbuzz-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed
<13>Aug 7 01:42:37 rpmi: libfreetype-2.10.2-alt1 sisyphus+251736.100.1.1 1589531898 installed
<13>Aug 7 01:42:37 rpmi: fontconfig-2.13.1-alt1 sisyphus+247349.100.1.2 1583841219 installed
Updating fonts cache: <29>Aug 7 01:42:38 fontconfig: Updating fonts cache: succeeded
[ DONE ]
<13>Aug 7 01:42:38 rpmi: libXft-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed
<13>Aug 7 01:42:38 rpmi: libcairo-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed
<13>Aug 7 01:42:38 rpmi: libpango-1.45.4-alt1 sisyphus+253017.160.8.1 1596208748 installed
<13>Aug 7 01:42:38 rpmi: libgtk+2-2.24.32-alt4 sisyphus+248211.200.2.1 1584869557 installed
<13>Aug 7 01:42:38 rpmi: libharfbuzz-icu-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed
<13>Aug 7 01:42:39 rpmi: libgail-2.24.32-alt4 sisyphus+248211.200.2.1 1584869557 installed
<13>Aug 7 01:42:39 rpmi: perl-Tk-804.034-alt1.2 sisyphus+219907.4300.1.1 1548345831 installed
<13>Aug 7 01:42:39 rpmi: libtk-8.6.10-alt1 sisyphus+241485.200.1.1 1574408419 installed
<13>Aug 7 01:42:39 rpmi: tk-8.6.10-alt1 sisyphus+241485.200.1.1 1574408419 installed
<13>Aug 7 01:42:39 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed
<13>Aug 7 01:42:41 rpmi: libgs-9.28-alt0.rc1.1 sisyphus+237325.100.1.1 1568103940 installed
<13>Aug 7 01:42:41 rpmi: ghostscript-common-9.28-alt0.rc1.1 sisyphus+237325.100.1.1 1568103940 installed
<13>Aug 7 01:42:41 rpmi: ghostscript-classic-9.28-alt0.rc1.1 sisyphus+237325.100.1.1 1568103940 installed
<13>Aug 7 01:42:41 rpmi: ghostscript-module-X-9.28-alt0.rc1.1 sisyphus+237325.100.1.1 1568103940 installed
<13>Aug 7 01:42:41 rpmi: libgd3-2.3.0-alt2 sisyphus+250375.100.2.1 1587542911 installed
<13>Aug 7 01:42:41 rpmi: fonts-type1-xorg-7.0.0-alt4 1188553211 installed
<13>Aug 7 01:42:42 rpmi: ttf2pt1-3.4.4-alt1.qa1 1366267504 installed
<13>Aug 7 01:42:42 rpmi: libharfbuzz-gobject-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed
<13>Aug 7 01:42:42 rpmi: xml-utils-1:2.9.10-alt3 sisyphus+245000.16400.79.1 1583229770 installed
<13>Aug 7 01:42:42 rpmi: rpm-build-gir-0.7.3-alt3 sisyphus+242150.100.1.1 1575312005 installed
<13>Aug 7 01:42:42 rpmi: ed-1:0.2-alt10 1449768441 installed
<13>Aug 7 01:42:42 rpmi: libdialog-1.3.20171209-alt1 1529583087 installed
<13>Aug 7 01:42:42 rpmi: dialog-1.3.20171209-alt1 1529583087 installed
<13>Aug 7 01:42:42 rpmi: libp11-kit-0.23.15-alt2 sisyphus+252784.100.2.2 1591274915 installed
<13>Aug 7 01:42:42 rpmi: libtasn1-4.16.0-alt1 sisyphus+245480.100.1.1 1580825069 installed
<13>Aug 7 01:42:42 rpmi: bc-1:1.07.1-alt1 sisyphus+221902.700.4.1 1550587848 installed
<13>Aug 7 01:42:42 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Aug 7 01:42:42 rpmi: alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Aug 7 01:42:42 rpmi: libnss-3.55.0-alt1 sisyphus+255566.200.1.1 1596128213 installed
<13>Aug 7 01:42:42 rpmi: ca-certificates-2020.06.29-alt1 sisyphus+254237.300.1.1 1593450881 installed
<13>Aug 7 01:42:42 rpmi: ca-trust-0.1.2-alt1 sisyphus+233348.100.1.1 1561653823 installed
<13>Aug 7 01:42:42 rpmi: p11-kit-trust-0.23.15-alt2 sisyphus+252784.100.2.2 1591274915 installed
<13>Aug 7 01:42:42 rpmi: libcrypto1.1-1.1.1g-alt1 sisyphus+249982.60.8.1 1587743567 installed
<13>Aug 7 01:42:42 rpmi: libssl1.1-1.1.1g-alt1 sisyphus+249982.60.8.1 1587743567 installed
<13>Aug 7 01:42:42 rpmi: libpython3-3.8.5-alt1 sisyphus+244405.100.3.1 1595544264 installed
<13>Aug 7 01:42:42 rpmi: python3-3.8.5-alt1 sisyphus+244405.100.3.1 1595544264 installed
<13>Aug 7 01:42:43 rpmi: python3-base-3.8.5-alt1 sisyphus+244405.100.3.1 1595544264 installed
<86>Aug 7 01:42:43 groupadd[252661]: group added to /etc/group: name=_keytab, GID=499
<86>Aug 7 01:42:43 groupadd[252661]: group added to /etc/gshadow: name=_keytab
<86>Aug 7 01:42:43 groupadd[252661]: new group: name=_keytab, GID=499
<13>Aug 7 01:42:43 rpmi: libkrb5-1.18.2-alt2 sisyphus+254565.100.4.1 1594375563 installed
<13>Aug 7 01:42:43 rpmi: glib2-devel-2.64.4-alt1 sisyphus+254365.100.1.1 1593701005 installed
<13>Aug 7 01:42:44 rpmi: libfreetype-devel-2.10.2-alt1 sisyphus+251736.100.1.1 1589531898 installed
<13>Aug 7 01:42:44 rpmi: libharfbuzz-devel-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed
<13>Aug 7 01:42:44 rpmi: fontconfig-devel-2.13.1-alt1 sisyphus+247349.100.1.2 1583841219 installed
<13>Aug 7 01:42:44 rpmi: python3-module-six-1.15.0-alt1 sisyphus+255738.100.2.1 1596527214 installed
<13>Aug 7 01:42:44 rpmi: libXft-devel-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed
<13>Aug 7 01:42:44 rpmi: libcairo-devel-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed
<13>Aug 7 01:42:44 rpmi: libtirpc-1.2.6-alt1 sisyphus+250076.100.1.1 1587038260 installed
<13>Aug 7 01:42:44 rpmi: libnsl2-1.1.0-alt1_1 1511548748 installed
<13>Aug 7 01:42:44 rpmi: python-modules-encodings-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-compiler-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-email-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-unittest-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-nis-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-xml-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-module-six-1.15.0-alt1 sisyphus+255738.100.2.1 1596527214 installed
<13>Aug 7 01:42:44 rpmi: python-module-pkg_resources-1:42.0.0-alt2 sisyphus+250566.100.6.1 1588187716 installed
<13>Aug 7 01:42:44 rpmi: python-modules-ctypes-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-multiprocessing-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-logging-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-modules-json-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-module-jinja2-2.11.2-alt1 sisyphus+254573.100.1.1 1594043344 installed
<13>Aug 7 01:42:44 rpmi: python-modules-hotshot-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-module-webencodings-0.5.1-alt2 sisyphus+245915.100.1.1 1581496070 installed
<13>Aug 7 01:42:44 rpmi: python-module-chardet-3.0.4-alt1 sisyphus+227476.1700.1.2 1555756717 installed
<13>Aug 7 01:42:44 rpmi: python-tools-2to3-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:44 rpmi: python-module-future-0.16.0-alt2 sisyphus+228356.200.3.3 1556645013 installed
<13>Aug 7 01:42:45 rpmi: python-module-pyglet-1.3.0-alt4.a1.hg20150730.1.1.1 1460413686 installed
<13>Aug 7 01:42:45 rpmi: python-module-whoosh-2.7.4-alt1 1527697941 installed
<13>Aug 7 01:42:45 rpmi: python-modules-bsddb-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:45 rpmi: python-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:45 rpmi: python-strict-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:45 rpmi: python-modules-distutils-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:45 rpmi: python-module-numpy-1:1.15.4-alt5 sisyphus+247694.100.3.3 1584382457 installed
<13>Aug 7 01:42:45 rpmi: python-module-cssselect-0.9.1-alt2 sisyphus+250566.2300.6.1 1588188959 installed
<13>Aug 7 01:42:45 rpmi: python-module-html5lib-1:1.0.1-alt1 sisyphus+238807.100.2.1 1570465973 installed
<13>Aug 7 01:42:45 rpmi: python-module-lxml-4.5.0-alt2 sisyphus+250566.2700.6.1 1588189447 installed
<13>Aug 7 01:42:45 rpmi: python-module-docutils-0.14-alt3 sisyphus+239215.40.2.1 1576588058 installed
<13>Aug 7 01:42:45 rpmi: python-module-idna-2.10-alt1 sisyphus+255040.100.1.1 1594995857 installed
<13>Aug 7 01:42:45 rpmi: python-module-pycparser-2.19-alt2 sisyphus+245734.100.1.1 1581192421 installed
<13>Aug 7 01:42:45 rpmi: python-module-cffi-1.14.0-alt1 sisyphus+255743.100.1.1 1596453352 installed
<13>Aug 7 01:42:45 rpmi: python-module-ntlm-1.1.0-alt1.2 sisyphus+228512.100.1.1 1556654575 installed
<13>Aug 7 01:42:46 rpmi: python-module-pytz-1:2020.1-alt1 sisyphus+254576.100.1.1 1594046074 installed
<13>Aug 7 01:42:46 rpmi: python-module-babel-1:2.6.0-alt1 sisyphus+228351.2400.6.2 1556652168 installed
<13>Aug 7 01:42:46 rpmi: python-module-PyStemmer-1.0.1-alt1.2.1 1321387369 installed
<13>Aug 7 01:42:46 rpmi: python-module-snowballstemmer-1.2.0-alt2.1 1457859319 installed
<13>Aug 7 01:42:46 rpmi: python-module-simplejson-3.15.0-alt3.qa1 sisyphus+245000.7400.78.1 1583199184 installed
<13>Aug 7 01:42:46 rpmi: python-module-ipaddress-1.0.18-alt2 sisyphus+245673.200.1.1 1581087895 installed
<13>Aug 7 01:42:46 rpmi: python-module-cryptography-3.0-alt1 sisyphus+255181.100.1.1 1595326568 installed
<13>Aug 7 01:42:46 rpmi: python-module-OpenSSL-19.0.0-alt1 sisyphus+238757.100.1.1 1570339901 installed
<13>Aug 7 01:42:46 rpmi: python-module-ndg-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed
<13>Aug 7 01:42:46 rpmi: python-module-ndg-httpsclient-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed
<13>Aug 7 01:42:46 rpmi: python-module-backports-3.5.0.1-alt1.1.1 1517645428 installed
<13>Aug 7 01:42:46 rpmi: python-module-backports.ssl_match_hostname-3.5.0.1-alt1.1.1 1517645428 installed
<13>Aug 7 01:42:46 rpmi: python-module-urllib3-2:1.25.10-alt1 sisyphus+255342.100.1.1 1595592746 installed
<13>Aug 7 01:42:46 rpmi: python-module-requests-2.23.0-alt1 sisyphus+248062.400.2.1 1584568195 installed
<13>Aug 7 01:42:46 rpmi: python-module-typing-3.6.6-alt2 sisyphus+220108.100.1.1 1548749697 installed
<13>Aug 7 01:42:46 rpmi: python-modules-sqlite3-2.7.18-alt1 sisyphus+255741.100.1.1 1596450428 installed
<13>Aug 7 01:42:47 rpmi: python-module-SQLAlchemy-1.3.18-alt1 sisyphus+254609.100.1.1 1594120587 installed
<13>Aug 7 01:42:47 rpmi: python-module-py-1.8.0-alt6 sisyphus+252790.200.2.1 1591264310 installed
<13>Aug 7 01:42:47 rpmi: python-module-mpmath-0.19-alt1.git20150621.1.1.1.1 sisyphus+227503.2100.1.3 1555860908 installed
<13>Aug 7 01:42:47 rpmi: python-module-sympy-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed
<13>Aug 7 01:42:48 rpmi: python-module-sympy-tests-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed
<13>Aug 7 01:42:48 rpmi: python-module-xapian-1.4.15-alt1 sisyphus+248304.200.4.1 1585071688 installed
<13>Aug 7 01:42:48 rpmi: python-module-sphinxcontrib-websupport-1.0.1-alt5 sisyphus+238085.40.2.1 1569316750 installed
<13>Aug 7 01:42:48 rpmi: python-module-alabaster-0.7.6-alt3 sisyphus+228351.700.4.1 1556637370 installed
<13>Aug 7 01:42:48 rpmi: python-module-Pygments-2.4.2-alt3 sisyphus+251222.100.1.1 1588756657 installed
<13>Aug 7 01:42:48 rpmi: python-module-sphinx-1:1.6.5-alt8 sisyphus+244988.100.1.1 1588163023 installed
<86>Aug 7 01:42:48 groupadd[255636]: group added to /etc/group: name=sasl, GID=498
<86>Aug 7 01:42:48 groupadd[255636]: group added to /etc/gshadow: name=sasl
<86>Aug 7 01:42:48 groupadd[255636]: new group: name=sasl, GID=498
<13>Aug 7 01:42:48 rpmi: libsasl2-3-2.1.27-alt2 sisyphus+228101.100.1.1 1556139861 installed
<13>Aug 7 01:42:48 rpmi: libldap-2.4.48-alt3 sisyphus+238816.100.1.1 1570449061 installed
<13>Aug 7 01:42:48 rpmi: libcurl-7.71.1-alt1 sisyphus+254403.100.1.1 1593776497 installed
<13>Aug 7 01:42:48 rpmi: libpoppler97-0.86.1-alt1 sisyphus+247631.100.1.1 1583927472 installed
<13>Aug 7 01:42:48 rpmi: python3-module-genshi-0.7-alt2 sisyphus+229363.100.1.1 1557847321 installed
<13>Aug 7 01:42:48 rpmi: python3-module-webencodings-0.5.1-alt2 sisyphus+245915.200.1.1 1581496105 installed
<13>Aug 7 01:42:48 rpmi: python3-module-html5lib-1:1.0.1-alt1 sisyphus+238807.100.2.1 1570465973 installed
<13>Aug 7 01:42:49 rpmi: python3-module-lxml-4.5.0-alt2 sisyphus+250566.2700.6.1 1588189447 installed
<13>Aug 7 01:42:49 rpmi: python3-module-cssselect-0.9.1-alt2 sisyphus+250566.2300.6.1 1588188959 installed
<13>Aug 7 01:42:49 rpmi: python3-module-javapackages-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed
<13>Aug 7 01:42:49 rpmi: rpm-build-java-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed
<13>Aug 7 01:42:49 rpmi: perl-Net-SSLeay-1.88-alt1 sisyphus+231287.100.1.1 1559389265 installed
<13>Aug 7 01:42:49 rpmi: perl-IO-Socket-SSL-2.068-alt1 sisyphus+248987.100.1.1 1585653153 installed
<13>Aug 7 01:42:49 rpmi: perl-Net-HTTPS-6.19-alt1 sisyphus+229756.100.1.1 1558454558 installed
<13>Aug 7 01:42:49 rpmi: perl-LWP-Protocol-https-6.07-alt1 1494527383 installed
<13>Aug 7 01:42:49 rpmi: ca-trust-java-0.1.2-alt1 sisyphus+233348.100.1.1 1561653823 installed
<13>Aug 7 01:42:52 rpmi: java-1.8.0-openjdk-headless-0:1.8.0.212.b04-alt2_0jpp8 sisyphus+255828.100.2.1 1596585080 installed
<13>Aug 7 01:42:53 rpmi: gambit-4.9.3-alt2 sisyphus+241636.100.1.1 1574697272 installed
<13>Aug 7 01:42:53 rpmi: foomatic-db-engine-4.0.12-alt1 1449527980 installed
<13>Aug 7 01:42:53 rpmi: ghostscript-utils-9.28-alt0.rc1.1 sisyphus+237325.100.1.1 1568103940 installed
<13>Aug 7 01:42:54 rpmi: texlive-2019-alt1_7 sisyphus+255755.100.1.1 1596460832 installed
<13>Aug 7 01:43:10 rpmi: texlive-collection-basic-2019-alt2_7 sisyphus+249628.100.1.1 1586387623 installed
<13>Aug 7 01:43:10 rpmi: texlive-texmf-2019-alt2_7 sisyphus+249628.100.1.1 1586387623 installed
<13>Aug 7 01:44:36 rpmi: texlive-dist-2019-alt2_7 sisyphus+249628.100.1.1 1586387623 installed
<13>Aug 7 01:44:36 rpmi: java-stub-javadoc-0.1-alt1 1229813340 installed
<13>Aug 7 01:44:36 rpmi: alsa-ucm-conf-1.2.3-alt1 sisyphus+253139.200.1.1 1591812001 installed
<13>Aug 7 01:44:36 rpmi: alsa-topology-conf-1.2.3-alt1 sisyphus+253139.100.1.1 1591811985 installed
<13>Aug 7 01:44:36 rpmi: libalsa-1:1.2.3.2-alt1 sisyphus+254690.100.1.1 1594280085 installed
<13>Aug 7 01:44:36 rpmi: java-1.8.0-openjdk-0:1.8.0.212.b04-alt2_0jpp8 sisyphus+255828.100.2.1 1596585080 installed
<13>Aug 7 01:44:37 rpmi: java-1.8.0-openjdk-devel-0:1.8.0.212.b04-alt2_0jpp8 sisyphus+255828.100.2.1 1596585080 installed
<13>Aug 7 01:44:37 rpmi: java-devel-default-1.7.0-alt1 1454012839 installed
<13>Aug 7 01:44:37 rpmi: libcurl-devel-7.71.1-alt1 sisyphus+254403.100.1.1 1593776497 installed
<13>Aug 7 01:44:37 rpmi: libpango-devel-1.45.4-alt1 sisyphus+253017.160.8.1 1596208748 installed
<13>Aug 7 01:44:37 rpmi: tk-devel-8.6.10-alt1 sisyphus+241485.200.1.1 1574408419 installed
<13>Aug 7 01:44:37 rpmi: gcc-c++-9-alt2 sisyphus+251923.100.2.2 1589881406 installed
<13>Aug 7 01:44:37 rpmi: gcc-fortran-9-alt2 sisyphus+251923.100.2.2 1589881406 installed
<13>Aug 7 01:44:37 rpmi: libXmu-devel-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed
<13>Aug 7 01:44:38 rpmi: makeinfo-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Aug 7 01:44:38 rpmi: liblapack-devel-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed
<13>Aug 7 01:44:38 rpmi: libgomp8-devel-8.4.1-alt1 sisyphus+247375.200.3.1 1583429212 installed
<13>Aug 7 01:44:38 rpmi: libpcre2-devel-10.35-alt1 sisyphus+251510.100.1.1 1589115548 installed
<13>Aug 7 01:44:38 rpmi: libtre-devel-0.8.0-alt2.2 sisyphus+249319.100.1.1 1585933005 installed
<13>Aug 7 01:44:38 rpmi: libtiff-devel-4.1.0-alt1 sisyphus+240802.100.1.1 1573743630 installed
<13>Aug 7 01:44:38 rpmi: texi2dvi-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Aug 7 01:44:38 rpmi: libjpeg-devel-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed
<13>Aug 7 01:44:38 rpmi: libreadline-devel-7.0.3-alt3 sisyphus+222164.300.1.1 1550686325 installed
<13>Aug 7 01:44:38 rpmi: liblzma-devel-5.2.5-alt1 sisyphus+249564.100.1.1 1586298197 installed
<13>Aug 7 01:44:38 rpmi: bzlib-devel-1:1.0.8-alt1 sisyphus+247226.100.1.1 1583187375 installed
Building target platforms: x86_64
Building for target x86_64
Wrote: /usr/src/in/nosrpm/R-base-4.0.2-alt1.nosrc.rpm
Installing R-base-4.0.2-alt1.src.rpm
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.82009
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ rm -rf R-4.0.2
+ echo 'Source #0 (R-4.0.2.tar):'
Source #0 (R-4.0.2.tar):
+ /bin/tar -xf /usr/src/RPM/SOURCES/R-4.0.2.tar
+ cd R-4.0.2
+ /bin/chmod -c -Rf u+rwX,go-w .
+ echo 'Patch #0 (R-4.0.2-alt1.patch):'
Patch #0 (R-4.0.2-alt1.patch):
+ /usr/bin/patch -p1
patching file .gear/rules
patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0
patching file .gear/tags/1af743c7e25d963067c0a7736c2f362bc1a54087
patching file .gear/tags/2c68f436cffd98cb9581510d928bea5942555c48
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/dbe24e8137437d3688e1d77cf1b67279d3099cea
patching file .gear/tags/e6f3c8b737583c5e27038507647866d029bfb5e4
patching file .gear/tags/ebdb5ee7ba9a5499c21aadcfee3318a7d6d52061
patching file .gear/tags/eef29626bf3bf68c9462ce5f0594fedd5a80168b
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/reg-tests-1c.R
patching file tests/reg-tests-1d.R
+ rm src/extra/blas/blas.f src/extra/blas/cmplxblas.f src/modules/lapack/cmplx.f src/modules/lapack/dlamch.f src/modules/lapack/dlapack.f src/modules/lapack/vecLibg95f.f
+ exit 0
Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.15620
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-4.0.2
+ 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=firefox ac_cv_path_R_PDFVIEWER=evince 'ac_cv_path_PAGER=less -isR' ac_cv_prog_R_PRINTCMD=lpr
+ lt_cv_prog_cc_static_works=no
+ ac_cv_path_R_ZIPCMD=zip
+ ac_cv_path_R_UNZIPCMD=unzip
+ ac_cv_path_R_BROWSER=firefox
+ ac_cv_path_R_PDFVIEWER=evince
+ ac_cv_path_PAGER='less -isR'
+ ac_cv_prog_R_PRINTCMD=lpr
+ CFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
+ export CFLAGS
+ CXXFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
+ export CXXFLAGS
+ FFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
+ export FFLAGS
+ FCFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
+ export FCFLAGS
+ '[' -n '' ']'
++ printf %s '-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g'
+ ASFLAGS=
+ export ASFLAGS
+ export lt_cv_deplibs_check_method=pass_all
+ lt_cv_deplibs_check_method=pass_all
+ 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 --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 --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-4.0'
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) firefox
using default browser ... firefox
checking for acroread... (cached) evince
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 x86_64-alt-linux-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-alt-linux-gcc accepts -g... yes
checking for x86_64-alt-linux-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether x86_64-alt-linux-gcc needs -traditional... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
looking for a modern Fortran compiler
checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether x86_64-alt-linux-gfortran accepts -g... yes
checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-alt-linux-g++ accepts -g... yes
checking whether x86_64-alt-linux-g++ -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing can compile C++ code... yes
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether x86_64-alt-linux-gcc accepts -fvisibility... yes
checking whether 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 we are using the GNU Objective C compiler... 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 readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking for tilde_expand_word... yes
checking whether rl_callback_sigcleanup exists and is declared... 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 ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for dlfcn.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking stdalign.h usability... yes
checking stdalign.h presence... yes
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checking errno.h presence... yes
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checking locale.h usability... yes
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checking stdbool.h usability... yes
checking stdbool.h presence... yes
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checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for x86_64-alt-linux-gcc option to accept ISO C99... none needed
checking for x86_64-alt-linux-gcc option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking 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... unsupported
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/9 -L/usr/lib64/gcc/x86_64-alt-linux/9/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/9/../../.. -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/9 -L/usr/lib64/gcc/x86_64-alt-linux/9/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/9/../../.. -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... unsupported
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... no
checking whether x86_64-alt-linux-g++ supports C++20 features with -std=gnu++2a... yes
checking for x86_64-alt-linux-g++ -std=gnu++11 option to support OpenMP... unsupported
checking for option providing pthread_kill... -pthread
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 sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... yes
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for __cospi... no
checking for __sinpi... no
checking for __tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... no
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether getline exists and is declared... yes
checking whether select exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether 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 thread.h usability... no
checking thread.h presence... no
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... none required
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... yes
checking whether mktime works correctly outside 1902-2037... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking for working ctanh... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_ in -lopenblas... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... no
checking for dpstrf_ in -llapack... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking 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 wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... yes
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... yes
checking X11/Xmu/Atoms.h presence... yes
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for /usr/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh
checking for /usr/lib64/tkConfig.sh... /usr/lib64/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking mmap support for zlib... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support suffices... yes
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking pcre2.h usability... yes
checking pcre2.h presence... 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 ... 7.71.1
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.28.0...
checking if libcurl supports https... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for lpr... (cached) lpr
checking for paperconf... /usr/bin/paperconf
checking for 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) unsupported
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for x86_64-alt-linux-ranlib... ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached)
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... bison
checking version of bison... 3.0.5, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory
checking whether OpenMP SIMD reduction is supported... no
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
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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 -fno-strict-aliasing
Fortran fixed-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
Default C++ compiler: x86_64-alt-linux-g++ -std=gnu++11 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
C++14 compiler: x86_64-alt-linux-g++ -std=gnu++14 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
C++17 compiler: x86_64-alt-linux-g++ -std=gnu++17 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
C++20 compiler: x86_64-alt-linux-g++ -std=gnu++2a -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
Fortran free-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -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 -j8
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-4.0.2/src/scripts'
creating src/scripts/R.fe
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/scripts'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/scripts'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/include'
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/include/R_ext'
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make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/include/R_ext'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making regerror.d from regerror.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
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making regexec.d from regexec.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making regcomp.d from regcomp.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-ast.d from tre-ast.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-compile.d from tre-compile.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-match-approx.d from tre-match-approx.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-match-backtrack.d from tre-match-backtrack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-mem.d from tre-mem.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-match-parallel.d from tre-match-parallel.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-stack.d from tre-stack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making tre-parse.d from tre-parse.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
making xmalloc.d from xmalloc.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/extra/tre'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
making interv.d from interv.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
making maxcol.d from maxcol.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
making integrate.d from integrate.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
making pretty.d from pretty.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
making uncmin.d from uncmin.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
making optim.d from optim.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c interv.c -o interv.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c maxcol.c -o maxcol.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpbfa.f -o dpbfa.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpbsl.f -o dpbsl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pretty.c -o pretty.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpodi.f -o dpodi.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dposl.f -o dposl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpoco.f -o dpoco.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dchdc.f -o dchdc.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpofa.f -o dpofa.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrls.f -o dqrls.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrutl.f -o dqrutl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrsl.f -o dqrsl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrdc.f -o dqrdc.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrco.f -o dtrco.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrsl.f -o dtrsl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dsvdc.f -o dsvdc.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c uncmin.c -o uncmin.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/appl'
#@make install-Linpack
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making mlutils.d from mlutils.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making fmin2.d from fmin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making i1mach.d from i1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making d1mach.d from d1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making fmax2.d from fmax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making fround.d from fround.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making fprec.d from fprec.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making ftrunc.d from ftrunc.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making sign.d from sign.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making imax2.d from imax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making fsign.d from fsign.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making imin2.d from imin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making chebyshev.d from chebyshev.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making log1p.d from log1p.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making lgammacor.d from lgammacor.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making stirlerr.d from stirlerr.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making gammalims.d from gammalims.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making gamma.d from gamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making bd0.d from bd0.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making lgamma.d from lgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making gamma_cody.d from gamma_cody.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making beta.d from beta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making lbeta.d from lbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making polygamma.d from polygamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making cospi.d from cospi.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making bessel_i.d from bessel_i.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making bessel_k.d from bessel_k.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making bessel_j.d from bessel_j.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making bessel_y.d from bessel_y.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making choose.d from choose.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making snorm.d from snorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making sexp.d from sexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dgamma.d from dgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pgamma.d from pgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qgamma.d from qgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rgamma.d from rgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dbeta.d from dbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pbeta.d from pbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qbeta.d from qbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rbeta.d from rbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dunif.d from dunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making punif.d from punif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qunif.d from qunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making runif.d from runif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dnorm.d from dnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pnorm.d from pnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rnorm.d from rnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qnorm.d from qnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dlnorm.d from dlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qlnorm.d from qlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making plnorm.d from plnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rlnorm.d from rlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making df.d from df.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pf.d from pf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qf.d from qf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rf.d from rf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dnf.d from dnf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dt.d from dt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pt.d from pt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qt.d from qt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dnt.d from dnt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rt.d from rt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pchisq.d from pchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dchisq.d from dchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qchisq.d from qchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rchisq.d from rchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rnchisq.d from rnchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pbinom.d from pbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dbinom.d from dbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qbinom.d from qbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rbinom.d from rbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dcauchy.d from dcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pcauchy.d from pcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qcauchy.d from qcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rmultinom.d from rmultinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rcauchy.d from rcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dexp.d from dexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pexp.d from pexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qexp.d from qexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rexp.d from rexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dgeom.d from dgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pgeom.d from pgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rgeom.d from rgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qgeom.d from qgeom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dhyper.d from dhyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making phyper.d from phyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qhyper.d from qhyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rhyper.d from rhyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dnbinom.d from dnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qnbinom.d from qnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pnbinom.d from pnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rnbinom.d from rnbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dpois.d from dpois.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making ppois.d from ppois.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qpois.d from qpois.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rpois.d from rpois.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dweibull.d from dweibull.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pweibull.d from pweibull.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qweibull.d from qweibull.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rweibull.d from rweibull.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dlogis.d from dlogis.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making plogis.d from plogis.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qlogis.d from qlogis.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dnchisq.d from dnchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making rlogis.d from rlogis.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pnchisq.d from pnchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qnchisq.d from qnchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making dnbeta.d from dnbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pnbeta.d from pnbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qnbeta.d from qnbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pnf.d from pnf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making pnt.d from pnt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qnf.d from qnf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qnt.d from qnt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making ptukey.d from ptukey.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making qtukey.d from qtukey.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
making wilcox.d from wilcox.c
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making toms708.d from toms708.c
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making signrank.d from signrank.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c d1mach.c -o d1mach.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fmax2.c -o fmax2.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fmin2.c -o fmin2.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnt.c -o qnt.o
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qtukey.c -o qtukey.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ptukey.c -o ptukey.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c signrank.c -o signrank.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c wilcox.c -o wilcox.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c toms708.c -o toms708.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
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 rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
config.status: creating src/unix/Makefile
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
making dynload.d from dynload.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
making Rembedded.d from Rembedded.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
making X11.d from X11.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
making system.d from system.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
making sys-std.d from sys-std.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
making sys-unix.d from sys-unix.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rembedded.c -o Rembedded.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dynload.c -o dynload.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c X11.c -o X11.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c system.c -o system.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sys-unix.c -o sys-unix.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sys-std.c -o sys-std.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-4.0.2"' \
-o Rscript ./Rscript.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
config.status: creating src/main/Makefile
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
making RNG.d from RNG.c
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making altrep.d from altrep.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
making Renviron.d from Renviron.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making CommandLineArgs.d from CommandLineArgs.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
making Rdynload.d from Rdynload.c
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making agrep.d from agrep.c
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making altclasses.d from altclasses.c
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
making apply.d from apply.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making arithmetic.d from arithmetic.c
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making attrib.d from attrib.c
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making bind.d from bind.c
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making character.d from character.c
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making builtin.d from builtin.c
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making array.d from array.c
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making coerce.d from coerce.c
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making colors.d from colors.c
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making complex.d from complex.c
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making context.d from context.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making datetime.d from datetime.c
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making cum.d from cum.c
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making dcf.d from dcf.c
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making connections.d from connections.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making debug.d from debug.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making deparse.d from deparse.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making devices.d from devices.c
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making dotcode.d from dotcode.c
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making dstruct.d from dstruct.c
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making duplicate.d from duplicate.c
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making dounzip.d from dounzip.c
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making engine.d from engine.c
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making edit.d from edit.c
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making envir.d from envir.c
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making errors.d from errors.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making format.d from format.c
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making gevents.d from gevents.c
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making gram-ex.d from gram-ex.c
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making eval.d from eval.c
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making gram.d from gram.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
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making graphics.d from graphics.c
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making identical.d from identical.c
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making grep.d from grep.c
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making inspect.d from inspect.c
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making inlined.d from inlined.c
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making internet.d from internet.c
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making iosupport.d from iosupport.c
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making lapack.d from lapack.c
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making localecharset.d from localecharset.c
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making list.d from list.c
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making logic.d from logic.c
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making mapply.d from mapply.c
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making main.d from main.c
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making match.d from match.c
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making names.d from names.c
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making memory.d from memory.c
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making options.d from options.c
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making objects.d from objects.c
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making paste.d from paste.c
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making plot.d from plot.c
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making plot3d.d from plot3d.c
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making plotmath.d from plotmath.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 print.d from print.c
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making printvector.d from printvector.c
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making printutils.d from printutils.c
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making qsort.d from qsort.c
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making radixsort.d from radixsort.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 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 scan.d from scan.c
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making seq.d from seq.c
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making serialize.d from serialize.c
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making sort.d from sort.c
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making source.d from source.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 startup.d from startup.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 subset.d from subset.c
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making summary.d from summary.c
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making sysutils.d from sysutils.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 version.d from version.c
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making g_alab_her.d from g_alab_her.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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making Rmain.d from Rmain.c
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making g_cntrlify.d from g_cntrlify.c
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making g_fontdb.d from g_fontdb.c
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making alloca.d from alloca.c
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making strncasecmp.d from strncasecmp.c
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making strdup.d from strdup.c
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making mkdtemp.d from mkdtemp.c
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Renviron.c -o Renviron.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c RNG.c -o RNG.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c altrep.c -o altrep.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rdynload.c -o Rdynload.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c apply.c -o apply.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c altclasses.c -o altclasses.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agrep.c -o agrep.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c builtin.c -o builtin.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c complex.c -o complex.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c character.c -o character.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bind.c -o bind.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c context.c -o context.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cum.c -o cum.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dcf.c -o dcf.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c debug.c -o debug.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c attrib.c -o attrib.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c arithmetic.c -o arithmetic.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c array.c -o array.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dstruct.c -o dstruct.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dounzip.c -o dounzip.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c edit.c -o edit.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coerce.c -o coerce.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c deparse.c -o deparse.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c duplicate.c -o duplicate.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c datetime.c -o datetime.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gevents.c -o gevents.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gram-ex.c -o gram-ex.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dotcode.c -o dotcode.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c errors.c -o errors.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c identical.c -o identical.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c inlined.c -o inlined.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c connections.c -o connections.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c summary.c -o summary.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c xxxpr.f -o xxxpr.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c subset.c -o subset.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c unique.c -o unique.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c subassign.c -o subassign.o
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c eval.c -o eval.o
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x86_64-alt-linux-gcc -shared -pthread -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 coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lopenblas -lgfortran -lm -lquadmath -lreadline -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
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mkdir -p -- /usr/src/RPM/BUILD/R-4.0.2/bin/exec
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mkdir -p -- /usr/src/RPM/BUILD/R-4.0.2/lib
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x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rmain.c -o Rmain.o
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x86_64-alt-linux-gcc -Wl,--export-dynamic -pthread -L"../../lib" -L/usr/local/lib64 -o R.bin Rmain.o -lR
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making rbitmap.d from rbitmap.c
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making Rsock.d from Rsock.c
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making rotated.d from rotated.c
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making Rhttpd.d from Rhttpd.c
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making Lapack.d from Lapack.c
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making internet.d from internet.c
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making libcurl.d from libcurl.c
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making nanoftp.d from nanoftp.c
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making sock.d from sock.c
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making nanohttp.d from nanohttp.c
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making sockconn.d from sockconn.c
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making devX11.d from devX11.c
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/internet'
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanoftp.c -o nanoftp.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanohttp.c -o nanohttp.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o
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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/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/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rbitmap.c -o rbitmap.o
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x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR
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mkdir -p -- /usr/src/RPM/BUILD/R-4.0.2/modules
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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/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/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rotated.c -o rotated.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Lapack.c -o Lapack.o
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x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o lapack.so Lapack.o -lR -llapack -lopenblas -lgfortran -lm -lquadmath
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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/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/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devX11.c -o devX11.o
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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 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm
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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/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/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dataentry.c -o dataentry.o
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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 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm
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mkdir -p -- ../../library
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building system startup profile
mkdir -p -- ../../../library/base/R
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building package 'translations'
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building package 'base'
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building package 'tools'
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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 http.d from http.c
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making text.d from text.c
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making signals.d from signals.c
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making Rmd5.d from Rmd5.c
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making install.d from install.c
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making getfmts.d from getfmts.c
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making gramRd.d from gramRd.c
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making gramLatex.d from gramLatex.c
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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 -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 -fno-strict-aliasing -c http.c -o http.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 -fno-strict-aliasing -c signals.c -o signals.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 -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/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c axis_scales.c -o axis_scales.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 -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 -fno-strict-aliasing -c colors.c -o colors.o
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making stem.d from stem.c
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make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
making plot.d from plot.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
making graphics.d from graphics.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
making par.d from par.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
making plot3d.d from plot3d.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
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 -fno-strict-aliasing -c init.c -o init.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
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 -fno-strict-aliasing -c stem.c -o stem.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
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 -fno-strict-aliasing -c base.c -o base.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
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 -fno-strict-aliasing -c graphics.c -o graphics.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
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 -fno-strict-aliasing -c par.c -o par.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
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 -fno-strict-aliasing -c plot3d.c -o plot3d.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
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 -fno-strict-aliasing -c plot.c -o plot.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/graphics'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making bandwidths.d from bandwidths.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making kmeans.d from kmeans.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making init.d from init.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making ansari.d from ansari.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making d2x2xk.d from d2x2xk.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making chisqsim.d from chisqsim.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making kendall.d from kendall.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making fexact.d from fexact.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making line.d from line.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making prho.d from prho.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making swilk.d from swilk.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making ks.d from ks.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making ksmooth.d from ksmooth.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making smooth.d from smooth.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making monoSpl.d from monoSpl.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making loessc.d from loessc.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making dblcen.d from dblcen.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making isoreg.d from isoreg.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making Srunmed.d from Srunmed.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making hclust-utils.d from hclust-utils.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making nls.d from nls.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making distance.d from distance.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making HoltWinters.d from HoltWinters.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
making rWishart.d from rWishart.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making PPsum.d from PPsum.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making burg.d from burg.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making arima.d from arima.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making filter.d from filter.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making mAR.d from mAR.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making pacf.d from pacf.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making starma.d from starma.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making port.d from port.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making family.d from family.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making sbart.d from sbart.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making approx.d from approx.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making massdist.d from massdist.c
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making loglin.d from loglin.c
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making lowess.d from lowess.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making complete_cases.d from complete_cases.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making splines.d from splines.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making lm.d from lm.c
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making fft.d from fft.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making deriv.d from deriv.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making cov.d from cov.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making fourier.d from fourier.c
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making model.d from model.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making integrate.d from integrate.c
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making optim.d from optim.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making optimize.d from optimize.c
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making zeroin.d from zeroin.c
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making rcont.d from rcont.c
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making random.d from random.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making distn.d from distn.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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making influence.d from influence.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c init.c -o init.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c kendall.c -o kendall.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c chisqsim.c -o chisqsim.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c bandwidths.c -o bandwidths.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c ansari.c -o ansari.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c kmeans.c -o kmeans.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c prho.c -o prho.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c line.c -o line.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/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 -fno-strict-aliasing -c swilk.c -o swilk.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c hclust.f -o hclust.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lminfl.f -o lminfl.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c kmns.f -o kmns.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stl.f -o stl.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 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c random.c -o random.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ppr.f -o ppr.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loessf.f -o loessf.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 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c model.c -o model.o
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x86_64-alt-linux-gfortran -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o
portsrc.f:2:34:
2 | LOGICAL FUNCTION STOPX(DUMMY)
| 1
Warning: Unused dummy argument 'dummy' at (1) [-Wunused-dummy-argument]
portsrc.f:6664:0:
6664 | NCOMP = NCOMP + 1
|
Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:6575:0:
6575 | INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC,
|
Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5522:0:
5522 | IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
|
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5659:0:
5659 | IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
|
Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10330:0:
10330 | IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
|
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10413:0:
10413 | V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
|
Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10325:0:
10325 | LK = DMAX1(LK, PHI*W(PHIPIN))
|
Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10467:0:
10467 | IF (KA .GE. KAMIN) GO TO 340
|
Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:12244:0:
12244 | V(NREDUC) = NRED
|
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:12247:0:
12247 | V(DST0) = DNWTST
|
Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2516:0:
2516 | V(NREDUC) = NRED
|
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2515:0:
2515 | 60 V(DST0) = DS0
|
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8175:0:
8175 | V(NREDUC) = NRED
|
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8174:0:
8174 | 90 V(DST0) = DS0
|
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8653:0:
8653 | 210 IV(FDH) = HES
|
Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:3588:0:
3588 | IF (LIV .LT. MIV2) GO TO 300
|
Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:12080:0:
12080 | 270 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
|
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:459:0:
459 | 300 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
|
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:367:0:
367 | CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
|
Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:367:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/stats/src'
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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 -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR
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byte-compiling package 'stats'
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building package 'datasets'
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
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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 -fno-strict-aliasing -c splines.c -o splines.o
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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 -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/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tcltk_unix.c -o tcltk_unix.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 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
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configuring Java ...
Java interpreter : /usr/lib/jvm/java/jre/bin/java
Java version : 1.8.0_212
Java home path : /usr/lib/jvm/java
Java compiler : /usr/lib/jvm/java/bin/javac
Java headers gen.: /usr/lib/jvm/java/bin/javah
Java archive tool: /usr/lib/jvm/java/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c conftest.c -o conftest.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib/jvm/java/jre/lib/amd64/server -ljvm -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
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JAVA_HOME : /usr/lib/jvm/java
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /usr/src/RPM/BUILD/R-4.0.2
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building all R object docs
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sample html
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srcfile html
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which html
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CRANtools html
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fileutils html
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package_native_routine_registration_skeleton
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demo html
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maintainer html
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make.socket html
memory.size html
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methods html
mirrorAdmin html
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sourceutils html
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converting help for package 'graphics'
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axis html
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identify html
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matplot html
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par html
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AIC html
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birthday html
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AirPassengers html
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Grid html
absolute.size html
arrow html
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current.viewport html
dataViewport html
depth html
deviceLoc html
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explode html
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grid.edit html
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grid.frame html
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grid.ls html
grid.move.to html
grid.newpage html
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grid.place html
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grid.record html
grid.rect html
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grid.segments html
grid.set html
grid.show.layout html
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grobCoords html
grobName html
grobWidth html
grobX html
legendGrob html
makeContent html
plotViewport html
resolveRasterSize html
showGrob html
showViewport html
stringWidth html
unit html
unit.c html
unit.length html
unit.pmin html
unit.rep html
unitType html
valid.just html
validDetails html
viewport html
viewports html
vpPath html
widthDetails html
xDetails html
xsplinePoints html
converting help for package 'splines'
asVector html
backSpline html
bs html
interpSpline html
ns html
periodicSpline html
polySpline html
predict.bSpline html
predict.bs html
splineDesign html
splineKnots html
splineOrder html
splines-package html
xyVector html
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coef-methods html
confint-methods html
logLik-methods html
mle-class html
mle html
plot-methods html
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stats4-package html
summary-methods html
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TclInterface html
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tkStartGUI html
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tkpager html
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compile html
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RngStream html
clusterApply html
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parallel-package html
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children html
mcaffinity html
mcfork html
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pvec html
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library'
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* installing *source* package 'codetools' ...
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converting help for package 'codetools'
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codetools html
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showTree html
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make[3]: Leaving directory '/usr/src/tmp/Rtmp3Kpdql/R.INSTALLb7e39734f9593/nnet/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp3Kpdql/R.INSTALLb7e39734f9593/nnet/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp3Kpdql/R.INSTALLb7e39734f9593/nnet/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'nnet'
finding HTML links ... done
class.ind html
multinom html
nnet.Hess html
nnet html
predict.nnet html
which.is.max html
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
* installing *source* package 'spatial' ...
** package 'spatial' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c krc.c -o krc.o
make[3]: Leaving directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pps.c -o pps.o
make[3]: Leaving directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpxvSt2m/R.INSTALLb7e1f696e0ad7/spatial/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c blkest.f -o blkest.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cp.f -o cp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgedi.f -o dgedi.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgefa.f -o dgefa.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgesl.f -o dgesl.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c linbin.f -o linbin.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c linbin2D.f -o linbin2D.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c locpoly.f -o locpoly.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlbin.f -o rlbin.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sdiag.f -o sdiag.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sstdiag.f -o sstdiag.o
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpRiAOFU/R.INSTALLb7d603c4a536a/KernSmooth/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c R_systat.c -o R_systat.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c SASxport.c -o SASxport.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c avl.c -o avl.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dbfopen.c -o dbfopen.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c file-handle.c -o file-handle.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c minitab.c -o minitab.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pfm-read.c -o pfm-read.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c spss.c -o spss.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sfm-read.c -o sfm-read.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stataread.c -o stataread.o
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
make[3]: Entering directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpHfZzcr/R.INSTALLb7d5a55cecebe/foreign/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c anova.c -o anova.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c anovapred.c -o anovapred.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c branch.c -o branch.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bsplit.c -o bsplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c choose_surg.c -o choose_surg.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fix_cp.c -o fix_cp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c free_tree.c -o free_tree.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gini.c -o gini.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c graycode.c -o graycode.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c insert_split.c -o insert_split.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mysort.c -o mysort.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nodesplit.c -o nodesplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c partition.c -o partition.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c poisson.c -o poisson.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c print_tree.c -o print_tree.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpart.c -o rpart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpartexp.c -o rpartexp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpcountup.c -o rpcountup.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rundown.c -o rundown.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rundown2.c -o rundown2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c surrogate.c -o surrogate.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c usersplit.c -o usersplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c xpred.c -o xpred.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c xval.c -o xval.o
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpIA1eSf/R.INSTALLb7d724254b58d/rpart/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpOihBGz/R.INSTALLb7d5b69298d13/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c MASS.c -o MASS.o
make[3]: Leaving directory '/usr/src/tmp/RtmpOihBGz/R.INSTALLb7d5b69298d13/MASS/src'
make[3]: Entering directory '/usr/src/tmp/RtmpOihBGz/R.INSTALLb7d5b69298d13/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lqs.c -o lqs.o
make[3]: Leaving directory '/usr/src/tmp/RtmpOihBGz/R.INSTALLb7d5b69298d13/MASS/src'
make[3]: Entering directory '/usr/src/tmp/RtmpOihBGz/R.INSTALLb7d5b69298d13/MASS/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpOihBGz/R.INSTALLb7d5b69298d13/MASS/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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
Rd warning: /usr/src/tmp/RtmpOihBGz/R.INSTALLb7d5b69298d13/MASS/man/pairs.lda.Rd:42: missing file link 'splom'
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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
begin installing recommended package cluster
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
begin installing recommended package class
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpgjcfQN/R.INSTALLbfa061d0d3c78/class/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c class.c -o class.o
make[3]: Leaving directory '/usr/src/tmp/RtmpgjcfQN/R.INSTALLbfa061d0d3c78/class/src'
make[3]: Entering directory '/usr/src/tmp/RtmpgjcfQN/R.INSTALLbfa061d0d3c78/class/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpgjcfQN/R.INSTALLbfa061d0d3c78/class/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpfjjcL1/R.INSTALLb7d611ed287b7/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfjjcL1/R.INSTALLb7d611ed287b7/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfjjcL1/R.INSTALLb7d611ed287b7/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c threeDplot.c -o threeDplot.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfjjcL1/R.INSTALLb7d611ed287b7/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfjjcL1/R.INSTALLb7d611ed287b7/lattice/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpfjjcL1/R.INSTALLb7d611ed287b7/lattice/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
begin installing recommended package Matrix
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
begin installing recommended package nlme
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dysta.f -o dysta.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c daisy.f -o daisy.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sildist.c -o sildist.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c spannel.c -o spannel.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mona.c -o mona.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fanny.c -o fanny.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c twins.c -o twins.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c clara.c -o clara.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pam.c -o pam.o
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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
Rd warning: /usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
clusplot.partition html
cluster-internal html
coef.hclust html
daisy html
diana html
dissimilarity.object html
ellipsoidhull html
Rd warning: /usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/man/ellipsoidhull.Rd:36: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/man/ellipsoidhull.Rd:87: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
fanny html
fanny.object html
flower html
lower.to.upper.tri.inds html
mona html
mona.object html
pam html
pam.object html
partition.object html
plantTraits html
plot.agnes html
Rd warning: /usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/man/plot.agnes.Rd:73: file link 'plot.dendrogram' in package 'stats' does not exist and so has been treated as a topic
plot.diana html
plot.mona html
plot.partition html
pltree html
pluton html
predict.ellipsoid html
print.agnes html
print.clara html
print.diana html
print.dissimilarity html
Rd warning: /usr/src/tmp/RtmpLVz8UT/R.INSTALLbfa0745b3b051/cluster/man/print.dissimilarity.Rd:27: file link 'print.dist' in package 'stats' does not exist and so has been treated as a topic
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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chol.f -o chol.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gnls.c -o gnls.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pythag.c -o pythag.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pdMat.c -o pdMat.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nlme.c -o nlme.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rs.f -o rs.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c corStruct.c -o corStruct.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nlmefit.c -o nlmefit.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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
Rd warning: /usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/man/plot.intervals.lmList.Rd:34: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/man/plot.intervals.lmList.Rd:21: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
plot.lmList html
plot.lme html
plot.nffGroupedData html
plot.nfnGroupedData html
plot.nmGroupedData html
plot.ranef.lmList html
plot.ranef.lme html
Rd warning: /usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/man/plot.ranef.lme.Rd:25: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/man/plot.ranef.lme.Rd:65: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/Rtmp5V5Hb7/R.INSTALLc1b42586aa36b/nlme/man/plot.ranef.lme.Rd:71: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
pooledSD html
predict.gls html
predict.gnls html
predict.lmList html
predict.lme html
predict.nlme html
print.summary.pdMat html
print.varFunc html
qqnorm.gls html
qqnorm.lme html
quinModel html
random.effects html
ranef.lmList html
ranef.lme html
reStruct html
recalc html
recalc.corStruct html
recalc.modelStruct html
recalc.reStruct html
recalc.varFunc html
residuals.gls html
residuals.glsStruct html
residuals.gnlsStruct html
residuals.lmList html
residuals.lme html
residuals.lmeStruct html
residuals.nlmeStruct html
simulate.lme html
solve.pdMat html
solve.reStruct html
splitFormula html
summary.corStruct html
summary.gls html
summary.lmList html
summary.lme html
summary.modelStruct html
summary.nlsList html
summary.pdMat html
summary.varFunc html
update.modelStruct html
update.varFunc html
varClasses html
varComb html
varConstPower html
varExp html
varFixed html
varFunc html
varIdent html
varPower html
varWeights html
varWeights.glsStruct html
varWeights.lmeStruct html
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c CHMfactor.c -o CHMfactor.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c TMatrix_as.c -o TMatrix_as.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Tsparse.c -o Tsparse.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cs_utils.c -o cs_utils.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chm_common.c -o chm_common.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgTMatrix.c -o dgTMatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgCMatrix.c -o dgCMatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dense.c -o dense.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Mutils.c -o Mutils.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpoMatrix.c -o dpoMatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dspMatrix.c -o dspMatrix.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtTMatrix.c -o dtTMatrix.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtCMatrix.c -o dtCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtpMatrix.c -o dtpMatrix.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Csparse.c -o Csparse.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrMatrix.c -o dtrMatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgeMatrix.c -o dgeMatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c factorizations.c -o factorizations.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
( cd Lib ; make clean )
( cd Source ; make clean )
( cd Source ; make clean )
make[3]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lgCMatrix.c -o lgCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ldense.c -o ldense.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
( cd Lib ; make -f "/usr/src/RPM/BUILD/R-4.0.2/etc/Makeconf" -f Makefile )
make[3]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c abIndex.c -o abIndex.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sparseQR.c -o sparseQR.o
In file included from /usr/src/RPM/BUILD/R-4.0.2/include/R.h:91,
from Mutils.h:12,
from sparseQR.h:4,
from sparseQR.c:1:
sparseQR.c: In function 'sparseQR_coef':
/usr/src/RPM/BUILD/R-4.0.2/include/R_ext/RS.h:74:25: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized]
74 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
| ^~~~~~~~~~
sparseQR.c:172:53: note: 'x' was declared here
172 | double *ax = REAL(GET_SLOT(ans, Matrix_xSym)), *x;
| ^
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
278 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
278 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_memory.c -o cholmod_memory.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
1408 | csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
| ^
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -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:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
488 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
| ^~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:48:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
In file included from ../Core/cholmod_dense.c:50:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
In file included from ../Core/cholmod_dense.c:52:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
303 | Int i, n, nz ;
| ^~
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
302 | double *Xx, *Xz ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Check/cholmod_write.c -o cholmod_write.o
../Check/cholmod_write.c: In function 'cholmod_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
365 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:108:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:110:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:112:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
345 | Int i, j, p, k, stype, nrow, ncol, nz, ok ;
| ^~
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
344 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
422 | Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
| ^~~~
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
419 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
419 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -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:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
114 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
| ^
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
40 | double *Lx, *Lz ;
| ^~
In file included from ../Core/cholmod_change_factor.c:118:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
40 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
265 | Int nsuper, xsize, ssize ;
| ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
680 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
680 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
679 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
679 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
827 | Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
| ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~~
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:124:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:126:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:131:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
In file included from ../Core/cholmod_transpose.c:136:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
207 | Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
| ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
961 | Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
| ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
1508 | ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
| ^~~
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
1506 | count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
| ^~~~~~~
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
1505 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
| ^~~~~~~~
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
1507 | jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
| ^~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
33 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
241 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
In file included from ../Supernodal/cholmod_super_solve.c:30:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
33 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
241 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
455 | Int totsize ;
| ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
In file included from ../Supernodal/cholmod_super_numeric.c:80:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
52 | 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 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
In file included from ../MatrixOps/cholmod_sdmult.c:50:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -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:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
278 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
278 | Int nrow, ncol, up, lo, values, diag, astype ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:48:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
In file included from ../Core/cholmod_dense.c:50:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
In file included from ../Core/cholmod_dense.c:52:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
30 | double *Ax, *Xx, *Az, *Xz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
136 | double *Xx, *Cx, *Xz, *Cz ;
| ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
229 | double *Xx, *Xz, *Yx, *Yz ;
| ^~
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
303 | Int i, n, nz ;
| ^~
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
302 | double *Xx, *Xz ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
488 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
| ^~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:108:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:110:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
In file included from ../Core/cholmod_triplet.c:112:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
31 | double *Rx, *Rz, *Tx, *Tz ;
| ^~
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
345 | Int i, j, p, k, stype, nrow, ncol, nz, ok ;
| ^~
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
344 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o
../Check/cholmod_write.c: In function 'cholmod_l_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
365 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
| ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
64 | double *Lx, *Yx, *Yz ;
| ^~
In file included from ../Cholesky/cholmod_solve.c:69:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
64 | double *Lx, *Yx, *Yz ;
| ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
337 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
40 | double *Lx, *Lz ;
| ^~
In file included from ../Core/cholmod_change_factor.c:118:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
40 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
265 | Int nsuper, xsize, ssize ;
| ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
680 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
680 | Int *Lp, *Li, *Lnz ;
| ^~
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
679 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
679 | double *Lx, *Lz ;
| ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
827 | Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
| ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~~
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
826 | Int *Ls, *Lpi, *Lpx, *Super, *Li ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:166:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:168:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:172:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:174:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:176:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -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:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
422 | Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
| ^~~~
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
419 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
419 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
| ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
In file included from ../Core/cholmod_transpose.c:124:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:126:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:131:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
45 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
142 | double *Ax, *Az, *Fx, *Fz ;
| ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
In file included from ../Core/cholmod_transpose.c:136:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
47 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
| ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
46 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
| ^~
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
143 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
114 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
| ^
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -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:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
207 | Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
| ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
961 | Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
| ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
1508 | ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
| ^~~
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
1506 | count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
| ^~~~~~~
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
1505 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
| ^~~~~~~~
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
1507 | jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
| ^~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:166:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:168:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:172:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:174:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
47 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
| ^~
In file included from ../Cholesky/cholmod_rowfac.c:176:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
51 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
| ^~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
455 | Int totsize ;
| ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
410 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
| ^~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
33 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
241 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
In file included from ../Supernodal/cholmod_super_solve.c:30:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
33 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
241 | nsrow2, n, ps2, j, i, d, nrhs ;
| ^
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -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:78:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
In file included from ../Supernodal/cholmod_super_numeric.c:80:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
111 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
52 | 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 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
52 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
| ^~
In file included from ../MatrixOps/cholmod_sdmult.c:50:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
55 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
| ^~~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
64 | double *Lx, *Yx, *Yz ;
| ^~
In file included from ../Cholesky/cholmod_solve.c:69:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
64 | double *Lx, *Yx, *Yz ;
| ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
337 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
| ^~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/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 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
410 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
| ^~~
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/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
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/CHOLMOD/Lib'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.0.2/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colamd_global.c -o colamd_global.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c colamd.c -o colamd_l.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colamd.c -o colamd.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/COLAMD/Source'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.0.2/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_1.c -o amd_i_1.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_control.c -o amd_i_control.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_order.c -o amd_i_order.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_global.c -o amd_i_global.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_2.c -o amd_i_2.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_info.c -o amd_i_info.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/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 amd_i_global.o amd_l_global.o
make[5]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/AMD/Source'
make[4]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -DNTIMER -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c SuiteSparse_config.c -o SuiteSparse_config.o
make[4]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/SuiteSparse_config'
make[4]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/SuiteSparse_config'
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src/SuiteSparse_config'
make[3]: Entering directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/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 CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
(from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix'
** help
*** installing help indices
converting help for package 'Matrix'
finding HTML links ... done
BunchKaufman-methods html
CAex html
CHMfactor-class html
Cholesky-class html
Cholesky html
CsparseMatrix-class html
Diagonal html
Hilbert html
KNex html
KhatriRao html
LU-class html
Matrix-class html
Matrix html
MatrixClass html
MatrixFactorization-class html
RsparseMatrix-class html
Schur-class html
Schur html
SparseM-conv html
Subassign-methods html
TsparseMatrix-class html
USCounties html
Xtrct-methods html
abIndex-class html
Rd warning: /usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/man/abIndex-class.Rd:80: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
abIseq html
all-methods html
all.equal-methods html
atomicVector-class html
band html
bandSparse html
bdiag html
boolean-matprod html
cBind html
chol html
chol2inv-methods html
colSums html
compMatrix-class html
condest html
dMatrix-class html
ddenseMatrix-class html
ddiMatrix-class html
denseMatrix-class html
dgCMatrix-class html
dgRMatrix-class html
dgTMatrix-class html
dgeMatrix-class html
diagU2N html
diagonalMatrix-class html
dpoMatrix-class html
drop0 html
dsCMatrix-class html
dsRMatrix-class html
dsparseMatrix-class html
dsyMatrix-class html
dtCMatrix-class html
dtRMatrix-class-def html
dtpMatrix-class html
dtrMatrix-class html
expand html
expm html
externalFormats html
facmul html
forceSymmetric html
formatSparseM html
generalMatrix-class html
graph2T html
image-methods html
Rd warning: /usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/man/image-methods.Rd:53: file link 'panel.levelplot.raster' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/man/image-methods.Rd:81: file link 'get.gpar' in package 'grid' does not exist and so has been treated as a topic
indMatrix-class html
index-class html
invPerm html
is.na-methods html
is.null.DN html
isSymmetric-methods html
isTriangular html
kronecker-methods html
ldenseMatrix-class html
ldiMatrix-class html
lgeMatrix-class html
lsparseMatrix-classes html
lsyMatrix-class html
ltrMatrix-class html
lu html
matrix-products html
Rd warning: /usr/src/tmp/Rtmp6m6CfY/R.INSTALLc1b4016d772e/Matrix/man/matrix-products.Rd:406: file link 'tcrossprod' in package 'base' does not exist and so has been treated as a topic
nMatrix-class html
ndenseMatrix-class html
nearPD html
ngeMatrix-class html
nnzero html
norm html
nsparseMatrix-classes html
nsyMatrix-class html
ntrMatrix-class html
number-class html
pMatrix-class html
printSpMatrix html
qr-methods html
rankMatrix html
rcond html
rep2abI html
replValue-class html
rleDiff-class html
rsparsematrix html
solve-methods html
spMatrix html
sparse.model.matrix html
sparseLU-class html
sparseMatrix-class html
sparseMatrix html
sparseQR-class html
sparseVector-class html
sparseVector html
symmetricMatrix-class html
symmpart html
triangularMatrix-class html
uniqTsparse html
unpack html
unused-classes html
updown html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
begin installing recommended package survival
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
begin installing recommended package mgcv
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agexact.c -o agexact.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agmart.c -o agmart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agfit5.c -o agfit5.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agmart3.c -o agmart3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agsurv4.c -o agsurv4.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agsurv3.c -o agsurv3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agscore2.c -o agscore2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agfit4.c -o agfit4.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agsurv5.c -o agsurv5.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chinv2.c -o chinv2.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cholesky2.c -o cholesky2.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chinv3.c -o chinv3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chsolve2.c -o chsolve2.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chsolve5.c -o chsolve5.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cholesky3.c -o cholesky3.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cholesky5.c -o cholesky5.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chsolve3.c -o chsolve3.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxcount1.c -o coxcount1.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c concordance1.c -o concordance1.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxmart2.c -o coxmart2.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxsafe.c -o coxsafe.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c concordance3.c -o concordance3.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxdetail.c -o coxdetail.o
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make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survreg7.c -o survreg7.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survfitkm.c -o survfitkm.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c zph1.c -o zph1.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c zph2.c -o zph2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/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 chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o concordance3.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 survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o zph1.o zph2.o -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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
Survmethods html
aareg html
aeqSurv html
agreg.fit html
aml html
anova.coxph html
attrassign html
basehaz html
bladder html
cch html
cgd html
cgd0 html
cipoisson html
Rd warning: /usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/man/cipoisson.Rd:59: file link 'ppois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpfzesEy/R.INSTALLe0b015e39cccb/survival/man/cipoisson.Rd:59: file link 'qpois' in package 'stats' does not exist and so has been treated as a topic
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
coxsurv.fit html
diabetic html
dsurvreg html
finegray html
flchain html
frailty 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
nafld html
neardate 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
pspline html
pyears html
quantile.survfit html
ratetable html
ratetableDate html
rats html
rats2 html
reliability html
residuals.coxph html
residuals.survreg html
retinopathy html
rhDNase html
ridge html
solder html
stanford2 html
statefig html
strata html
summary.aareg html
summary.coxph html
summary.pyears html
summary.survexp html
summary.survfit html
survConcordance-deprecated 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-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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
begin installing recommended package boot
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxph.c -o coxph.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mgcv.c -o mgcv.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c misc.c -o misc.o
misc.c: In function 'tweedious':
misc.c:321:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
321 | if (j_max>j_hi) j_max = j_hi; if (j_max<j_lo) j_max = j_lo;
| ^~
misc.c:321:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
321 | if (j_max>j_hi) j_max = j_hi; if (j_max<j_lo) j_max = j_lo;
| ^~
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mvn.c -o mvn.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c soap.c -o soap.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qp.c -o qp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c magic.c -o magic.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tprs.c -o tprs.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c discrete.c -o discrete.o
discrete.c: In function 'Xbd0':
discrete.c:366: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
366 | #pragma omp critical (xbdcalloc)
|
discrete.c:389: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
389 | #pragma omp critical (xbdcalloc)
|
discrete.c:411: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
411 | #pragma omp critical (xbdcalloc)
|
discrete.c: In function 'Xbd':
discrete.c:432: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
432 | #pragma omp critical (xbdcalloc)
|
discrete.c:469: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
469 | #pragma omp critical (xbdcalloc)
|
discrete.c:493: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
493 | #pragma omp critical (xbdcalloc)
|
discrete.c: In function 'XWXd0':
discrete.c:1535:5: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
1535 | XWXijs(XWX+tpsu[rb] + (ptrdiff_t) nxwx * tpsu[cb],rb,cb,r,c,X,k,ks,m,p,*nx,*n,ts, dt,*nt,w,ws,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1536 | tri,off,work + tid * q,worki + tid * (ptrdiff_t) qi,nxwx,ht,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1537 | sm + tid * (ptrdiff_t) *n,SMstack + 3 * tid * (ptrdiff_t) *n ); /* compute r,c block */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
discrete.c: In function 'XWXd1':
discrete.c:1796:5: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
1796 | XWXijs(XWX+tpsur[rb] + (ptrdiff_t) nxwx * tpsuc[cb],rb,cb,r,c,X,k,ks,m,p,*nx,*n,ts, dt,*nt,w,ws,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1797 | tri,off,work + tid * q,worki + tid * (ptrdiff_t) qi,nxwx,ht,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1798 | sm + tid * (ptrdiff_t) *n,SMstack + 3 * tid * (ptrdiff_t) *n ); /* compute r,c block */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mat.c -o mat.o
mat.c: In function 'chol_up':
mat.c:1877:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1877 | if (*n>1) R[1] = -2.0;return; /* signals error */
| ^~
mat.c:1877:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1877 | if (*n>1) R[1] = -2.0;return; /* signals error */
| ^~~~~~
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sparse-smooth.c -o sparse-smooth.o
sparse-smooth.c: In function 'Rkdnearest':
sparse-smooth.c:996:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
996 | if (!dim_sym) dim_sym = install("dim");if (!dist_sym) dist_sym = install("dist");
| ^~
sparse-smooth.c:996:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
996 | if (!dim_sym) dim_sym = install("dim");if (!dist_sym) dist_sym = install("dist");
| ^~
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gdi.c -o gdi.o
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.2/lib -L/usr/local/lib64 -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.0.2/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/src'
installing to /usr/src/RPM/BUILD/R-4.0.2/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
FFdes html
Predict.matrix html
Predict.matrix.cr.smooth html
Predict.matrix.soap.film html
Rrank html
Sl.initial.repara html
Sl.repara html
Sl.setup html
Tweedie html
XWXd html
anova.gam html
bam html
Rd warning: /usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/man/bam.Rd:14: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/man/bam.Rd:129: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/man/bam.Rd:188: file link 'makeForkCluster' in package 'parallel' does not exist and so has been treated as a topic
bam.update html
bandchol html
blas.thread.test html
bug.reports.mgcv html
cSplineDes html
chol.down html
choose.k html
columb html
concurvity html
coxph html
coxpht html
dDeta html
exclude.too.far html
extract.lme.cov html
family.mgcv html
fix.family.link html
fixDependence html
formXtViX html
formula.gam html
fs.test html
full.score html
gam html
gam.check html
gam.control html
gam.convergence html
gam.fit html
gam.fit3 html
gam.fit5.post.proc html
gam.models html
gam.outer html
gam.reparam html
gam.scale html
gam.selection html
gam.side html
gam.vcomp html
gam2objective html
gamObject html
gamSim html
gamlss.etamu html
gamlss.gH html
gamm html
gammals html
gaulss html
get.var html
gevlss html
ginla html
identifiability html
in.out html
inSide html
influence.gam html
initial.sp html
interpret.gam html
jagam html
k.check html
ldTweedie html
ldetS html
linear.functional.terms html
logLik.gam html
ls.size html
magic html
magic.post.proc html
mgcv-FAQ html
mgcv-package html
mgcv-parallel html
Rd warning: /usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/man/mgcv-parallel.Rd:11: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
mini.roots html
missing.data html
model.matrix.gam html
mono.con html
mroot html
multinom html
mvn html
negbin html
new.name html
notExp html
notExp2 html
null.space.dimension html
ocat html
one.se.rule html
pcls html
pdIdnot html
pdTens html
pen.edf html
place.knots html
plot.gam html
polys.plot html
predict.bam html
Rd warning: /usr/src/tmp/RtmpER3Cbn/R.INSTALLe0aff6906da64/mgcv/man/predict.bam.Rd:77: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
predict.gam html
print.gam html
qq.gam html
rTweedie html
random.effects html
residuals.gam html
rig html
rmvn html
s html
scat html
sdiag html
single.index html
slanczos html
smooth.construct html
smooth.construct.ad.smooth.spec html
smooth.construct.bs.smooth.spec html
smooth.construct.cr.smooth.spec html
smooth.construct.ds.smooth.spec html
smooth.construct.fs.smooth.spec html
smooth.construct.gp.smooth.spec html
smooth.construct.mrf.smooth.spec html
smooth.construct.ps.smooth.spec html
smooth.construct.re.smooth.spec html
smooth.construct.so.smooth.spec html
smooth.construct.sos.smooth.spec html
smooth.construct.t2.smooth.spec html
smooth.construct.tensor.smooth.spec html
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[31] [32] Appendix A [33] [34] [35]
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t/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr9.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm
/cmsl10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb>
</usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf-dist/fonts
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t12.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
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[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13]
[14]
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[]@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de
vel[] @textrm and @texttt make
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[]@texttt Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"),
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[22] [23] [24] [25] [26] Chapter 7 [27] [28] [29] Chapter 8 [30] Chapter 9
[31] [32] Appendix A [33] [34] [35]
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[]@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
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[36] [37] [38] [39] [40] [41] [42] [43] [44] Appendix B [45] [46] [47] [48]
[49] [50] Appendix C [51] [52] [53] [54] [55] [56]
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[58] [59] [60]
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amsfonts/cm/cmbx12.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cm
csc10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></us
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dist/fonts/type1/public/amsfonts/cm/cmmi9.pfb></usr/share/texmf-dist/fonts/type
1/public/amsfonts/cm/cmr10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfon
ts/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
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pe1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsy10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmt
i10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/s
hare/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texmf-dis
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[] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M
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[44] Chapter 8 [45] [46]
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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
[47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10
[58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index)
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atrix 1.2-6[]
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ics with methods[]
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[16] [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] Chapter 7 [43]
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solves to
[44] Chapter 8 [45] [46]
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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
[47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10
[58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index)
[62] [63] (Concept index) [64] [65] )
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[] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
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[16] [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] Chapter 7 [43]
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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
[44] Chapter 8 [45] [46]
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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
[47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10
[58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index)
[62] [63] (Concept index) [64] [65] )
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[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
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[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
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found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51] [52]
(Concept Index) [53] Appendix A [54] [55] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51] [52]
(Concept Index) [53] Appendix A [54] [55] )
(see the transcript file for additional information)</usr/share/texmf-dist/font
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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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/QQ.pdf> [35] [36] </usr/src/RPM/BUILD/R-4.0.2/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
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ual/images/fig12.pdf> [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14
[78] [79]
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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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/QQ.pdf> [35] [36] </usr/src/RPM/BUILD/R-4.0.2/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]
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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] [94] [95] Appendix E [96] [97]
Appendix F [98] [99] )
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Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] </us
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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] [94] [95] Appendix E [96] [97]
Appendix F [98] [99] )
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[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
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[76] [77] [78] [79] [80]
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lename@texttt }[] @textrm and
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[83] [84] [85] [86] Chapter 3 [87] [88] [89] [90] [91] [92] [93] [94]
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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
3[] @textrm are fast ver-sions of R's
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[151] Chapter 6 [152] [153] [154] [155] [156] [157] [158] [159] [160] [161]
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Chapter 7 [174] [175] Chapter 8 [176] [177] [178]
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nst char *);[]
[180] [181] [182] [183] [184] [185]
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[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] [18] [19] [20] [21]
[22] [23] [24] [25] [26]
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[]@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
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[]@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[]
[27] [28] [29] [30]
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[] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[]
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49]
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[]@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX
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[50] [51] [52] [53]
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[]@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
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[]@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor
version 52.0[]
[54]
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@texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b
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[55] [56] [57] [58] [59] [60] [61]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[62] [63] [64] [65] [66] [67] Chapter 2 [68] [69] [70] [71] [72] [73] [74]
[75] [76] [77] [78] [79]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[80] [81]
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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
[82] [83] [84] [85] Chapter 3 [86] [87] [88] [89] [90] [91] [92] [93]
Chapter 4 [94] [95] [96] [97] [98]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[99] [100] [101] [102]
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[103]
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[109]
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[]@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to
INTEGER(4)[]
Chapter 5 [110] [111] [112] [113] [114] [115] [116] [117] [118] [119]
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[]
[120] [121] [122] [123] [124] [125]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
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[149]
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[]
[150] Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160]
[161] [162] [163] [164] [165] [166] Warning: unbalanced parentheses in @def...
[167] [168] [169] [170] [171] [172]
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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 [173] [174] Chapter 8 [175] [176] [177]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[178]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[179] [180] [181] [182] [183] [184]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[185] [186]
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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) [187] [188] [189] [190]
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(/usr/src/RPM/BUILD/R-4.0.2/doc/manual/R-exts.toc) (Acknowledgements)
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[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] [18] [19] [20] [21]
[22] [23] [24] [25] [26]
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[]@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[]
[27] [28] [29] [30]
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[] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[]
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49]
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[]@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX
PICFLAGS`[]
[50] [51] [52] [53]
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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[]
[54]
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@texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b
e looked for
[55] [56] [57] [58] [59] [60] [61]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[62] [63] [64] [65] [66] [67] Chapter 2 [68] [69] [70] [71] [72] [73] [74]
[75] [76] [77] [78] [79]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[80] [81]
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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
[82] [83] [84] [85] Chapter 3 [86] [87] [88] [89] [90] [91] [92] [93]
Chapter 4 [94] [95] [96] [97] [98]
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[99] [100] [101] [102]
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on [-Wlto-type-mismatch][]
[109]
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ration [-Wlto-type-mismatch][]
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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 [110] [111] [112] [113] [114] [115] [116] [117] [118] [119]
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[]
[120] [121] [122] [123] [124] [125]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[149]
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[]
[150] Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160]
[161] [162] [163] [164] [165] [166] Warning: unbalanced parentheses in @def...
[167] [168] [169] [170] [171] [172]
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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 [173] [174] Chapter 8 [175] [176] [177]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[178]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[179] [180] [181] [182] [183] [184]
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tive in-stall and
[185] [186]
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[]@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
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exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25] [26] [27]
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[28] [29] [30] [31]
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[32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46]
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version 52.0[]
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[55] [56] [57] [58] [59] [60] [61] [62]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[63] [64] [65] [66] [67] [68] Chapter 2 [69] [70] [71] [72] [73] [74] [75]
[76] [77] [78] [79] [80]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[81] [82]
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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
[83] [84] [85] [86] Chapter 3 [87] [88] [89] [90] [91] [92] [93] [94]
Chapter 4 [95] [96] [97] [98] [99]
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[100] [101] [102] [103]
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[]@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to
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[121] [122] [123] [124] [125] [126] [127]
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" -lpackB[]
[128] [129] [130] [131] [132] [133] [134] [135] [136]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
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[149]
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NilValue);[]
[150]
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[]
[151] Chapter 6 [152] [153] [154] [155] [156] [157] [158] [159] [160] [161]
[162] [163] [164] [165] [166] [167] Warning: unbalanced parentheses in @def...
[168] [169] [170] [171] [172] [173]
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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 [174] [175] Chapter 8 [176] [177] [178]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[179]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[180] [181] [182] [183] [184] [185]
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tive in-stall and
[186] [187]
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-core\R32[] @textrm or
(Function and variable index) [188] [189] [190] [191]
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pfb>
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defuns, macros, cross references, insertions,
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(/usr/src/RPM/BUILD/R-4.0.2/doc/manual/R-exts.toc) (Acknowledgements)
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[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] [18] [19] [20] [21]
[22] [23] [24] [25] [26]
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[]@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[]
[27] [28] [29] [30]
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[] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[]
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49]
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[]@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX
PICFLAGS`[]
[50] [51] [52] [53]
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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[]
[54]
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@texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b
e looked for
[55] [56] [57] [58] [59] [60] [61]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[62] [63] [64] [65] [66] [67] Chapter 2 [68] [69] [70] [71] [72] [73] [74]
[75] [76] [77] [78] [79]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[80] [81]
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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
[82] [83] [84] [85] Chapter 3 [86] [87] [88] [89] [90] [91] [92] [93]
Chapter 4 [94] [95] [96] [97] [98]
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[99] [100] [101] [102]
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[103]
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-overflow[]
[104]
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pper bound of 0[]
[105] [106] [107] [108]
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on [-Wlto-type-mismatch][]
[109]
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ration [-Wlto-type-mismatch][]
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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 [110] [111] [112] [113] [114] [115] [116] [117] [118] [119]
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[]
[120] [121] [122] [123] [124] [125]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[149]
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[]
[150] Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160]
[161] [162] [163] [164] [165] [166] Warning: unbalanced parentheses in @def...
[167] [168] [169] [170] [171] [172]
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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 [173] [174] Chapter 8 [175] [176] [177]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[178]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[179] [180] [181] [182] [183] [184]
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tive in-stall and
[185] [186]
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(Function and variable index) [187] [188] [189] [190]
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r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att
ributes assigned to @textsl
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mf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texmf-dist/fonts/
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(/usr/src/RPM/BUILD/R-4.0.2/doc/manual/R-exts.aux) Chapter 1 [1]
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[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] [18] [19] [20] [21]
[22] [23] [24] [25] [26]
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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 $(SOURCES:.cpp=.o)[]
[27] [28] [29] [30]
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[] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[]
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49]
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[]@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX
PICFLAGS`[]
[50] [51] [52] [53]
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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[]
[54]
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@texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b
e looked for
[55] [56] [57] [58] [59] [60] [61]
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[]@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[]
[62] [63] [64] [65] [66] [67] Chapter 2 [68] [69] [70] [71] [72] [73] [74]
[75] [76] [77] [78] [79]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[80] [81]
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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
[82] [83] [84] [85] Chapter 3 [86] [87] [88] [89] [90] [91] [92] [93]
Chapter 4 [94] [95] [96] [97] [98]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
e.g.
[99] [100] [101] [102]
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[]@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[]
[103]
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
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[]@texttt bound-strict,float-cast-overflow,float-divide-by-zero,signed-integer
-overflow[]
[104]
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[]@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[]
[105] [106] [107] [108]
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[]@texttt boot.f:61: warning: type of 'ddot' does not match original declarati
on [-Wlto-type-mismatch][]
[109]
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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 [110] [111] [112] [113] [114] [115] [116] [117] [118] [119]
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[]@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[]
[120] [121] [122] [123] [124] [125]
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[]@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[]
[126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148]
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[] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[]
[149]
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[]@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[]
[150] Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160]
[161] [162] [163] [164] [165] [166] Warning: unbalanced parentheses in @def...
[167] [168] [169] [170] [171] [172]
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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 [173] [174] Chapter 8 [175] [176] [177]
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[]@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[]
[178]
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[]@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[]
[179] [180] [181] [182] [183] [184]
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@texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[185] [186]
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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) [187] [188] [189] [190]
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[6] [7]
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[8] [9] [10]
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rel.diff.=",[]
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[16] [17] [18] [19] [20]
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tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
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[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
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[32] [33] [34] [35]
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[36] [37]
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
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[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
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[38]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[39] [40]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2669--2669
[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3337--3337
[]\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",[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3369--3369
[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
[51]
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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 3377--3377
[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3380--3380
[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
[52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3820--3822
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 4061--4061
[] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive)
[62] [63] [64]
Underfull \hbox (badness 4927) in paragraph at lines 4319--4323
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
Underfull \hbox (badness 2012) in paragraph at lines 4319--4323
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[65] [66]
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
[67]
Underfull \hbox (badness 4595) in paragraph at lines 4468--4471
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4626--4626
[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
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[] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e
xclude = TRUE)[]
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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
[70] [71] [72]
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5097--5099
[]\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
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5509--5517
[]\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
[82] [83] [84] [85] [86] [87] [88] [89] [90]
Underfull \hbox (badness 1796) in paragraph at lines 6075--6083
[]\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 : / /
[91] [92]
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 6271--6271
[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6272--6272
[]\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}[]
[93] [94]
Underfull \hbox (badness 1242) in paragraph at lines 6411--6415
\T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel
ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment.
[95]
Underfull \hbox (badness 1635) in paragraph at lines 6474--6477
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
Underfull \hbox (badness 3009) in paragraph at lines 6478--6481
[]\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
[96]
Underfull \hbox (badness 1308) in paragraph at lines 6521--6529
[]\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
[97] [98]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6685--6685
[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
Underfull \vbox (badness 10000) has occurred while \output is active [99]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6735--6737
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 :
[100]
Underfull \hbox (badness 1997) in paragraph at lines 6862--6867
[]\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1
0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x
zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC
onnection\T1/ptm/m/n/10 ,
[101]
Underfull \hbox (badness 10000) in paragraph at lines 6900--6903
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 6900--6903
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[102] [103]
Underfull \hbox (badness 1406) in paragraph at lines 7082--7088
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
Underfull \hbox (badness 2173) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and
web-pages gen-er-ated by
Underfull \hbox (badness 2134) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 7102--7104
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[104]
Underfull \hbox (badness 1067) in paragraph at lines 7144--7151
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[105] [106]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 7346--7346
[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[108] [109]
Underfull \hbox (badness 1231) in paragraph at lines 7471--7477
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the
first el-e-
[110] [111] [112]
Underfull \hbox (badness 10000) in paragraph at lines 7683--7685
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[113] [114]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7828--7828
[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
[115] [116] [117] [118]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8066--8066
[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[119] [120]
Underfull \hbox (badness 10000) in paragraph at lines 8188--8198
[]\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 8188--8198
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
is a generic func-tion, meth-ods can be
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8220--8225
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[121] [122] [123] [124] [125] [126] [127]
Underfull \hbox (badness 1629) in paragraph at lines 8709--8721
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8709--8721
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
, and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[128] [129] [130] [131] [132] [133]
Underfull \hbox (badness 10000) in paragraph at lines 9157--9161
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[134]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9248--9248
[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9250--9250
[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
[135]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9277--9277
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[136] [137]
Underfull \hbox (badness 5403) in paragraph at lines 9414--9416
[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9433--9435
[]\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
[138] [139] [140]
Underfull \hbox (badness 1603) in paragraph at lines 9658--9661
[]\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
[141] [142] [143] [144] [145] [146] [147] [148] [149]
Underfull \hbox (badness 1917) in paragraph at lines 10266--10271
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[150]
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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 10322--10322
[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[151] [152]
Underfull \hbox (badness 1168) in paragraph at lines 10424--10429
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
Underfull \hbox (badness 10000) in paragraph at lines 10463--10469
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
Underfull \hbox (badness 5403) in paragraph at lines 10470--10473
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[153] [154]
Underfull \hbox (badness 2828) in paragraph at lines 10629--10633
[][][]$\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 10629--10633
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
[155]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10662--10662
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[156]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10735--10735
[]\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, ..[]
[157] [158]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10882--10882
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[159] [160] [161]
Underfull \hbox (badness 6396) in paragraph at lines 11079--11087
[]\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 11088--11090
[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[162] [163] [164]
Underfull \hbox (badness 10000) in paragraph at lines 11305--11308
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[165] [166] [167] [168] [169] [170] [171] [172] [173]
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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
[174]
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
and
Underfull \hbox (badness 10000) in paragraph at lines 12077--12079
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[175] [176]
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 12199--12203
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[177] [178]
Underfull \hbox (badness 10000) in paragraph at lines 12314--12316
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13159--13159
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[190] [191] [192] [193] [194] [195]
Underfull \hbox (badness 2221) in paragraph at lines 13609--13618
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
Underfull \hbox (badness 1635) in paragraph at lines 13609--13618
\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[196] [197] [198] [199]
Underfull \hbox (badness 2253) in paragraph at lines 13870--13872
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[200] [201]
Underfull \hbox (badness 2573) in paragraph at lines 13987--13989
[]\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 =
[202] [203]
Underfull \hbox (badness 10000) in paragraph at lines 14142--14144
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[204] [205]
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14270--14273
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \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[]
[206]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[207]
Underfull \hbox (badness 10000) in paragraph at lines 14410--14413
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14420--14420
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[208]
Underfull \hbox (badness 10000) in paragraph at lines 14486--14489
[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
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:[]
[209]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
Underfull \hbox (badness 1472) in paragraph at lines 14556--14563
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14556--14563
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14564--14568
[]\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,
[210] [211] [212]
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[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14729--14729
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
[213] [214] [215]
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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[]
[216]
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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
[217]
Underfull \hbox (badness 6944) in paragraph at lines 15146--15149
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[218]
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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),[]
[219] [220]
Underfull \hbox (badness 10000) in paragraph at lines 15309--15311
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
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[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15335--15335
[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[]
[221]
Underfull \hbox (badness 2790) in paragraph at lines 15342--15345
[]\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
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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
[222]
Underfull \hbox (badness 10000) in paragraph at lines 15448--15450
[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls
Underfull \hbox (badness 4954) in paragraph at lines 15448--15450
\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
in this
Underfull \hbox (badness 10000) in paragraph at lines 15470--15475
[]\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/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-rides
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
[223]
Underfull \hbox (badness 10000) in paragraph at lines 15482--15486
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
Underfull \hbox (badness 10000) in paragraph at lines 15482--15486
\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 15487--15495
[]\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
[224]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15595--15595
[]\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[]
Underfull \vbox (badness 10000) has occurred while \output is active [225]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 15617--15617
[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
[226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16435--16435
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[238]
Underfull \hbox (badness 2418) in paragraph at lines 16544--16548
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
,
Underfull \hbox (badness 6510) in paragraph at lines 16551--16554
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
[239]
Underfull \hbox (badness 2326) in paragraph at lines 16586--16593
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[240] [241] [242]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16836--16836
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
[243]
Underfull \hbox (badness 1867) in paragraph at lines 16861--16868
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[244] [245] [246] [247]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17139--17139
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
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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 17219--17219
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
[249] [250] [251] [252]
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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)))
[253]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17651--17651
[]\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[]
[254] [255] [256]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17841--17841
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[257] [258] [259] [260]
Underfull \hbox (badness 2435) in paragraph at lines 18109--18111
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
[261]
Underfull \hbox (badness 2285) in paragraph at lines 18175--18177
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18183--18183
[]\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.[]
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[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[262] [263]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
[264]
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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" :[]
[265] [266]
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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):[]
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 18702--18704
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[270] [271] [272] [273] [274] [275] [276] [277]
Underfull \hbox (badness 4699) in paragraph at lines 19275--19278
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[278] [279]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19403--19403
[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[280] [281]
Underfull \hbox (badness 4739) in paragraph at lines 19538--19540
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[282]
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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)[]
[283] [284] [285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1975) in paragraph at lines 20166--20169
[]\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
[291] [292] [293] [294] [295] [296]
Underfull \hbox (badness 1077) in paragraph at lines 20564--20569
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
[297]
Underfull \hbox (badness 10000) in paragraph at lines 20578--20585
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[298]
Underfull \hbox (badness 10000) in paragraph at lines 20652--20656
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[299] [300]
Underfull \hbox (badness 10000) in paragraph at lines 20801--20805
[]\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 20801--20805
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 20806--20813
[]\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-
[301] [302]
Underfull \hbox (badness 10000) in paragraph at lines 20937--20944
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[303]
Underfull \hbox (badness 10000) in paragraph at lines 21058--21062
[]\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
[304]
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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
Underfull \hbox (badness 6592) in paragraph at lines 21128--21133
\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 21128--21133
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 21128--21133
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[305] [306] [307]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21295--21295
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21299--21299
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[308]
Underfull \hbox (badness 3343) in paragraph at lines 21360--21364
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[309] [310]
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[] \T1/pcr/m/n/9 identical(L$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,
pr = 0.2))),[]
[311] [312]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 21624--21624
[]\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-
[313]
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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
[314]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21790--21790
[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
[315] [316]
Underfull \hbox (badness 1400) in paragraph at lines 21958--21962
[][][]\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 do
uble[][][] \T1/ptm/m/n/10 (class
[317] [318] [319]
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[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
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\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
Underfull \hbox (badness 4531) in paragraph at lines 22128--22134
\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[320] [321] [322] [323] [324] [325] [326] [327] [328]
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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 ))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 22770--22770
[]\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)[]
[329] [330]
Underfull \hbox (badness 1655) in paragraph at lines 22894--22898
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
[331] [332] [333] [334]
Underfull \hbox (badness 2277) in paragraph at lines 23143--23146
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
\T1/ptm/m/n/10 are typ-i-cally prefer-able.
[335] [336]
Underfull \hbox (badness 10000) in paragraph at lines 23272--23275
[]\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc
r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.
0,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 1484) in paragraph at lines 23724--23732
[]\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 /
[343] [344]
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[345] [346] [347] [348] [349] [350] [351]
Underfull \hbox (badness 1448) in paragraph at lines 24310--24318
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[352] [353]
Underfull \hbox (badness 3849) in paragraph at lines 24425--24430
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[354]
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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-re-spond-
ing
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\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE))
\T1/ptm/m/n/10 which are also given by
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[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10
. If the en-vi-ron-ment is used as a hash
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[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
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\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[355] [356]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[357] [358] [359]
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[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[360] [361] [362]
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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-
[363] [364] [365] [366] [367]
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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-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
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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-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about 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 com-p
uted 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)
[368]
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
[369]
Underfull \hbox (badness 10000) in paragraph at lines 25488--25494
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
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\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
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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:[]
[370] [371] [372]
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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
[][][]
[373] [374] [375]
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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');
[376] [377] [378] [379]
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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
[380] [381]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 26346--26354
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[382] [383]
Underfull \hbox (badness 3271) in paragraph at lines 26565--26568
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[384] [385] [386]
Underfull \hbox (badness 3138) in paragraph at lines 26865--26871
[]\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 26865--26871
\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 26865--26871
\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 26878--26881
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
[387]
Underfull \hbox (badness 1389) in paragraph at lines 26904--26906
[]\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
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[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
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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
[388]
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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 26981--26987
\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 26981--26987
\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 26981--26987
\T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina
ry.universal" \T1/ptm/m/n/10 are no longer
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[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
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\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
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\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 26996--27003
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[389] [390] [391] [392]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 27344--27344
[]\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 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
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\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[394] [395]
Underfull \hbox (badness 10000) in paragraph at lines 27504--27507
[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
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\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[396] [397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27782--27788
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
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[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
\T1/ptm/m/n/10 which con-cate-nates and
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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[]
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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)[]
[400] [401] [402]
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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 =
[403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1817) in paragraph at lines 28379--28383
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m
/n/10 get[][][](name,envir =
[409]
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[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
see
[410] [411] [412]
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[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[413] [414] [415] [416] [417] [418] [419] [420] [421] [422]
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[] \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))[]
[423] [424]
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[426]
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[]\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"[]
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[]\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 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
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[428]
Underfull \hbox (badness 7415) in paragraph at lines 29725--29729
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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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[]
[429]
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[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
[430]
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[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[431] [432]
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\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
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\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 /
[433] [434]
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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
[435] [436]
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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 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[437] [438]
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[]\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")[]
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[]\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")[]
[439]
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[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
[440] [441] [442] [443] [444]
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[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
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\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 30843--30848
\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 ,
[445] [446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 2080) in paragraph at lines 31380--31390
[]\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.[]
[453] [454] [455] [456] [457] [458] [459]
Underfull \hbox (badness 7558) in paragraph at lines 31920--31924
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 31930--31932
[]\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
Underfull \hbox (badness 5417) in paragraph at lines 31935--31938
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 31939--31941
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 31942--31944
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[460] [461] [462] [463] [464] [465]
Underfull \hbox (badness 10000) in paragraph at lines 32347--32351
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[466] [467] [468] [469] [470]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32703--32703
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32706--32706
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
[471] [472] [473] [474] [475] [476] [477]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 33146--33146
[] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[]
[478] [479] [480] [481] [482] [483]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33581--33581
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[484] [485]
Underfull \hbox (badness 1158) in paragraph at lines 33685--33690
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1762) in paragraph at lines 33712--33718
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal
and hex-adec-i-mal rep-re-sen-ta-tions
[486] [487]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 33870--33870
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[488] [489] [490]
Underfull \hbox (badness 8151) in paragraph at lines 34130--34133
[]\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 .
[491] [492] [493] [494]
Underfull \hbox (badness 10000) in paragraph at lines 34345--34350
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10
gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by =
[495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506]
[507] [508] [509]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 35333--35333
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[510] [511] [512]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 35585--35585
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 35587--35587
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[513]
Underfull \hbox (badness 4954) in paragraph at lines 35630--35636
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 35630--35636
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[514] [515]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 35741--35741
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[516] [517] [518] [519]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36074--36074
[]\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)[]
[520]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36089--36089
[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[521] [522] [523] [524] [525] [526]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 36530--36530
[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
Overfull \hbox (12.78088pt too wide) in paragraph at lines 36531--36531
[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
[527] [528] [529]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 36798--36798
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[530] [531]
Underfull \hbox (badness 6110) in paragraph at lines 36889--36899
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 36889--36899
\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
Underfull \hbox (badness 1237) in paragraph at lines 36889--36899
\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 36889--36899
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n 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 36889--36899
\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
Underfull \hbox (badness 10000) in paragraph at lines 36935--36941
[]\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 36935--36941
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 36935--36941
\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 36947--36954
[]\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 36947--36954
\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 36947--36954
\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
[532] [533] [534] [535]
Underfull \hbox (badness 1484) in paragraph at lines 37179--37183
[]\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/
m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
[536]
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
[537] [538] [539] [540] [541] [542] [543] [544]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 37821--37821
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[545] [546] [547]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 38069--38069
[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[548]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38113--38113
[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[549] [550] [551] [552] [553] [554] [555]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 38547--38547
[]\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, ....[]
[556]
Underfull \hbox (badness 10000) in paragraph at lines 38601--38608
[]\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 38601--38608
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38654--38654
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[557] [558] [559] [560] [561]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 38965--38965
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[562] [563] [564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39130--39130
[]\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.
Overfull \hbox (20.58041pt too wide) in paragraph at lines 39168--39168
[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
[565]
Underfull \hbox (badness 2293) in paragraph at lines 39198--39204
[]\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 39198--39204
\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 39217--39222
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 39217--39222
\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
[566]
Underfull \hbox (badness 2452) in paragraph at lines 39307--39310
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 39307--39310
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[567] [568] [569]
Underfull \hbox (badness 10000) in paragraph at lines 39495--39499
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
Underfull \hbox (badness 1584) in paragraph at lines 39510--39513
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[570] [571]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 39642--39642
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[572]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 39712--39712
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used
[573] [574] [575]
Underfull \hbox (badness 1082) in paragraph at lines 39856--39859
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577]
Underfull \hbox (badness 1038) in paragraph at lines 40047--40050
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[578] [579] [580] [581] [582] [583]
Underfull \hbox (badness 1442) in paragraph at lines 40408--40412
\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 =
[584] [585] [586]
Underfull \hbox (badness 4096) in paragraph at lines 40658--40661
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[587] [588]
Underfull \hbox (badness 7888) in paragraph at lines 40772--40776
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
length(bin) >
[589] [590]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40926--40926
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 40928--40928
[] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[]
[591]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40930--40930
[] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 40943--40945
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[592]
Underfull \hbox (badness 10000) in paragraph at lines 41023--41026
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[593] [594]
Underfull \hbox (badness 3872) in paragraph at lines 41141--41144
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[595]
Underfull \hbox (badness 5475) in paragraph at lines 41207--41211
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[596] [597] [598] [599] [600] [601]
Underfull \hbox (badness 10000) in paragraph at lines 41625--41632
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 41681--41690
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 41681--41690
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
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[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 41691--41699
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
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\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[602]
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\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[603]
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[][][]$\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-
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[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[604] [605] [606]
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[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[607] [608]
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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:[]
[609] [610]
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[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
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[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
[611] [612] [613]
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[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
, and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[614] [615]
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
[616]
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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 e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
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\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
[617]
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[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
and sup-press-ing the print-ing of er-ror mes-sages;
[618]
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[]\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 42834--42846
\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 ,
[619] [620] [621] [622]
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[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[623] [624] [625] [626] [627] [628] [629]
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[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
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[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[]
[630]
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[][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[
][][]\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 ,
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[][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex
ists[][][]\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 ,
[631] [632]
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[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
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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
[633] [634] [635]
Underfull \hbox (badness 3668) in paragraph at lines 44072--44074
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[636] [637]
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[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[638]
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[]\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 ...[]
[639] [640]
Underfull \hbox (badness 6220) in paragraph at lines 44391--44396
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
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\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
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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 , namely a m
a-trix whose rows each
[641] [642]
Underfull \hbox (badness 2818) in paragraph at lines 44508--44514
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
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[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[643] [644]
Underfull \hbox (badness 1622) in paragraph at lines 44637--44639
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[645] [646] [647] [648] [649]
Underfull \hbox (badness 2846) in paragraph at lines 45000--45004
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[650]
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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-dard
' reg-exps, in-clud-ing el-e-ments named
[651]) (./compiler-pkg.tex [652]
Chapter 2.
[653]
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 be us
ed 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 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[654] [655] [656]) (./datasets-pkg.tex
Chapter 3.
[657] [658] [659] [660] [661]
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[662]
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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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[664] [665] [666] [667]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[668] [669]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 835--838
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[670] [671]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\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.
[672] [673]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1146--1149
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[674] [675] [676] [677] [678]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456
[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[679] [680]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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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-tained from the a
bove
[681] [682] [683]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[684]
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[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
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[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[685] [686]
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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]]))))[]
[687] [688] [689] [690]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2152--2155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[691] [692] [693]
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[694] [695] [696] [697] [698]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[699]
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[700]
Underfull \vbox (badness 2376) has occurred while \output is active [701]
[702]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[703] [704]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[705]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[706] [707] [708] [709] [710] [711] [712]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[713] [714]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[715]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[716]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[717]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
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[]\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 /
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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729]
[730] [731]) (./grDevices-pkg.tex [732]
Chapter 4.
[733] [734] [735] [736]
Underfull \hbox (badness 1365) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
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[]\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/ptm/m/n/1
0 in
[737] [738]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[739] [740]
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
Underfull \hbox (badness 5175) in paragraph at lines 1186--1188
[]\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
[751] [752] [753]
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
Underfull \hbox (badness 1173) in paragraph at lines 1399--1402
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[754] [755] [756] [757] [758] [759] [760] [761]
Underfull \hbox (badness 1565) in paragraph at lines 1887--1892
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1887--1892
\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
[762]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
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[]\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-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[763] [764]
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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
[765] [766]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[767] [768]
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\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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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
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[769] [770]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
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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)
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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)[]
[772] [773] [774] [775] [776]
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Underfull \vbox (badness 10000) has occurred while \output is active [777]
[778] [779] [780] [781]
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[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[782]
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[]\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv",
scale.in = 255))[]
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[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[783] [784]
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[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[785] [786]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3558--3558
[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[]
[787]
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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)[]
[788]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
[789]
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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 ,
[790]
Underfull \hbox (badness 2189) in paragraph at lines 3815--3820
[]\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we
ll 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$[][]\T1/ptm/m/n/10 .
[791]
Underfull \vbox (badness 10000) has occurred while \output is active [792]
Underfull \hbox (badness 5260) in paragraph at lines 3983--3986
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[793] [794] [795] [796] [797]
Underfull \hbox (badness 5939) in paragraph at lines 4315--4320
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[798] [799] [800] [801] [802] [803]
Underfull \hbox (badness 10000) in paragraph at lines 4719--4724
[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
/ devnet / actionscript /
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\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[804] [805]
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[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[806] [807]
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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
[808]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5063--5063
[]\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 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[809]
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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"
[810]
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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
[811] [812] [813]
Underfull \hbox (badness 7344) in paragraph at lines 5459--5461
[]\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 5470--5474
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[814] [815]
Underfull \hbox (badness 1552) in paragraph at lines 5596--5605
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[816]
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[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[817] [818]
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[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[819]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
[820] [821]
Underfull \hbox (badness 10000) in paragraph at lines 5963--5965
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
for on-screen de-vices and to
[822] [823] [824] [825] [826]
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[]\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
sep = "."))[]
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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[827] [828] [829] [830] [831] [832]
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[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
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[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
[833] [834] [835] [836]
Underfull \hbox (badness 10000) in paragraph at lines 6949--6954
[]\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 y
pos\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 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[837]
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[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
[838]
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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 :
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[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
[839]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[840]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
[841]
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[842]
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[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[843]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[844] [845]
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\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 /
[846] [847]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[848] [849] [850]) (./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 =
[851] [852] [853]
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[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[854] [855] [856] [857]
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[] \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
[858] [859]
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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[]
[860]
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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
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[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[861] [862]
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
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[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
[863] [864] [865]
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[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/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-able.
Overfull \hbox (106.98032pt too wide) in paragraph at lines 981--981
[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[]
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[]\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 985--985
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
[866] [867] [868] [869]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1269--1269
[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
[870] [871] [872]
Underfull \hbox (badness 1024) in paragraph at lines 1431--1439
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
Underfull \hbox (badness 3375) in paragraph at lines 1465--1467
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[873] [874]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1535--1535
[]\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 1536--1536
[]\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 1542--1542
[]\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 1543--1543
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[875] [876] [877] [878] [879]
Underfull \hbox (badness 10000) in paragraph at lines 1846--1852
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10
contourplot[][][] \T1/ptm/m/n/10 (and
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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 = "")[]
[880] [881]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[882] [883]
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[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, 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))[]
[884] [885]
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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 = "",[]
[886]
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[]\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
[887]
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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
[888]
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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[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
[889]
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[]\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[]
[890] [891] [892]
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[893]
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[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[894] [895]
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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
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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 :[]
[896]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[897] [898] [899]
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[]\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, ...)[]
[900] [901]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
raster im-ages are used when the
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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")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[902] [903] [904]
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[]\T1/pcr/m/n/9 barplot(yhist$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"),[]
[905]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[906] [907]
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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])[]
[908]
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[] \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 [909]
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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))[]
[910]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[911] [912]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4044--4044
[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[913] [914]
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[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
[915]
Underfull \hbox (badness 3930) in paragraph at lines 4277--4279
[]\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
[916] [917] [918] [919] [920]
Underfull \hbox (badness 1286) in paragraph at lines 4588--4591
\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
[921] [922]
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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))[]
[923]
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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/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[924] [925]
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[926] [927]
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[928 </usr/src/RPM/BUILD/R-4.0.2/library/graphics/help/figures/mai.pdf>]
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[929 </usr/src/RPM/BUILD/R-4.0.2/library/graphics/help/figures/oma.pdf>]
[930]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[931]
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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,[]
Underfull \vbox (badness 10000) has occurred while \output is active [932]
[933] [934] [935] [936] [937]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5830--5830
[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5831--5831
[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
[938]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again>
\relax
l.5890 \aliasA{plot}{plot.default}{plot}
[939] [940] [941] [942] [943]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6222--6222
[]\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[]
[944] [945] [946] [947] [948] [949]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[950] [951]
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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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[][]
[952 </usr/src/RPM/BUILD/R-4.0.2/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,[]
[953]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
Underfull \vbox (badness 10000) has occurred while \output is active [954]
[955]
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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)))))[]
[956]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[957] [958] [959] [960]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7367--7367
[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[961] [962] [963] [964] [965] [966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7754--7754
[]\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):[]
[967]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[968] [969] [970] [971] [972]
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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,[]
[973] [974] [975]
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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, ...)[]
[976] [977]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
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[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[978]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[979]
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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),[]
[980] [981]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[982] [983]
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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...")[]
[984]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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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 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[985]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8968 \HeaderA{units}{Graphical Units}{units}
[986]
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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
[987] [988]
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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)[]
[989]) (./grid-pkg.tex [990]
Chapter 6.
[991] [992] [993] [994] [995] [996] [997] [998]
Underfull \hbox (badness 10000) in paragraph at lines 476--482
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117
[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1009] [1010] [1011] [1012]
Underfull \hbox (badness 3219) in paragraph at lines 1380--1383
[]\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
[1013] [1014] [1015] [1016] [1017] [1018]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1768--1768
[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[1019] [1020] [1021]
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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")[]
[1022]
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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 ,
[1023]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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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
[1024] [1025] [1026]
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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
[1027] [1028] [1029]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1030]
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
[1031] [1032]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[1033] [1034] [1035] [1036]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[1037] [1038] [1039] [1040] [1041]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1042]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
"bottom")))[]
[1043]
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1044] [1045]
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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,[]
[1046] [1047] [1048]
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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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[1061]
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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
[1062]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1063] [1064] [1065]
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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 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
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[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
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\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1086] [1087] [1088] [1089] [1090]
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
[1091]
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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
[1092]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1093] [1094]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
do-ing some-thing like \T1/pcr/m/n/10 depth
[1095]
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[1097] [1098]
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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"))))[]
[1099]) (./methods-pkg.tex [1100]
Chapter 7.
[1101] [1102]
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\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1103] [1104] [1105]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1106] [1107]
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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[]
[1108]
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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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[1122] [1123] [1124]
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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[]
[1125] [1126]
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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 c
an be an ob-ject of class
[1127] [1128] [1129]
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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 =
[1130] [1131]
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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
[1132] [1133] [1134]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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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
[1135]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1136] [1137] [1138]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1139] [1140] [1141] [1142] [1143] [1144] [1145]
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[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
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\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1146] [1147]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1148]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these
classes takes spe-cial ar-gu-ments
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[]
[1149] [1150]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
=
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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1151]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
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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
[1152] [1153] [1154]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1155] [1156] [1157]
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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,[]
[1158]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1159] [1160] [1161]
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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 ,
[1162] [1163] [1164]
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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
[1165] [1166] [1167] [1168]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1169]
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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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[1171]
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[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1172] [1173]
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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
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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/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1183] [1184]
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
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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
[1185]
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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
[1186] [1187]
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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
[1188]
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[1190] [1191]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6973 \aliasA{S4}{S3Part}{S4}
[1192]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
[1193] [1194]
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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")[]
[1195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again>
\relax
l.7229 \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.7231 \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.7232 \aliasA{Math}{S4groupGeneric}{Math}
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th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.7234 \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.7235 \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
[1196]
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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/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
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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 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
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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 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1197] [1198]
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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 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1199] [1200]
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\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
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[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
\T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1212]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1213]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697
[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1214] [1215] [1216] [1217]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959
[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1218] [1219] [1220]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167
[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1221] [1222] [1223]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429
[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
[1224] [1225] [1226] [1227]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737
[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1228]
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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 9858--9858
[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238]
Underfull \hbox (badness 10000) in paragraph at lines 10556--10558
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\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 10564--10568
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1239] [1240] [1241]) (./parallel-pkg.tex [1242]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1243]
Underfull \hbox (badness 4242) in paragraph at lines 96--98
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1244] [1245]
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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
[1246] [1247] [1248]
Underfull \hbox (badness 10000) in paragraph at lines 449--451
[]\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
[1249] [1250] [1251] [1252] [1253]
Underfull \hbox (badness 1917) in paragraph at lines 755--764
[]\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 755--764
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1254]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 848--848
[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1255] [1256] [1257]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1039--1039
[]\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 1043--1043
[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1258] [1259]
Underfull \hbox (badness 5388) in paragraph at lines 1158--1163
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 1182--1190
[]\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
[1260]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1219--1219
[]\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)[]
[1261]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1335--1335
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
[1262]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1349--1349
[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
Underfull \hbox (badness 1577) in paragraph at lines 1378--1381
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1263]
Underfull \hbox (badness 3375) in paragraph at lines 1425--1427
[]\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
[1264] [1265]) (./splines-pkg.tex [1266]
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
[1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1275]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
-1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1276] [1277]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1278] [1279] [1280]) (./stats-pkg.tex
Chapter 10.
[1281]
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 o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
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[]
[1282] [1283] [1284] [1285] [1286]
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[]
[1287]
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)
[1288] [1289] [1290] [1291] [1292] [1293]
Underfull \hbox (badness 1024) in paragraph at lines 879--881
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303]
Underfull \hbox (badness 10000) in paragraph at lines 1541--1545
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1541--1545
\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1541--1545
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1304]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1617--1617
[] \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 1620--1620
[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
[1305] [1306]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767
[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
[1307]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1779--1779
[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$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 :[
]
[1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318]
[1319] [1320]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2770--2770
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1321] [1322] [1323] [1324]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3010--3010
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1325] [1326] [1327]
Underfull \hbox (badness 10000) in paragraph at lines 3220--3222
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1328]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3269--3269
[]\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 3270--3270
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1329] [1330] [1331] [1332] [1333] [1334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3661--3661
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1335] [1336] [1337] [1338]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3940--3940
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1339] [1340] [1341] [1342] [1343]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4229--4229
[]\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 4230--4230
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1344] [1345] [1346]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4469--4469
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1347] [1348] [1349]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4644--4644
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1350]
Underfull \hbox (badness 3989) in paragraph at lines 4738--4745
[]\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 =
[1351] [1352] [1353] [1354] [1355] [1356]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5123--5123
[]\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 5125--5125
[]\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))[]
[1357] [1358] [1359]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5346--5346
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5364--5364
[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
Underfull \hbox (badness 2680) in paragraph at lines 5391--5393
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is
given by
[1360] [1361] [1362]
Underfull \hbox (badness 1436) in paragraph at lines 5574--5579
[]\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 5574--5579
\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 5574--5579
\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 ,
[1363] [1364] [1365]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5777--5777
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1366] [1367] [1368]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5944--5944
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1369] [1370] [1371]
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[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1372]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6237--6237
[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
[1373]
Underfull \hbox (badness 10000) in paragraph at lines 6304--6309
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1374] [1375] [1376] [1377]
Underfull \hbox (badness 5954) in paragraph at lines 6500--6502
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1378]
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[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6586--6588
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6589--6594
\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,
Underfull \hbox (badness 7238) in paragraph at lines 6625--6628
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1379]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6660--6660
[]\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 6675--6675
[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6690--6690
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
Underfull \vbox (badness 10000) has occurred while \output is active [1380]
[1381] [1382] [1383]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6934--6934
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1384] [1385] [1386] [1387] [1388] [1389]
Underfull \hbox (badness 10000) in paragraph at lines 7333--7337
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1390]
Underfull \hbox (badness 6493) in paragraph at lines 7432--7435
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1391] [1392]
Underfull \hbox (badness 10000) in paragraph at lines 7569--7572
[]\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 =
[1393] [1394] [1395] [1396] [1397] [1398] [1399]
Underfull \hbox (badness 10000) in paragraph at lines 7981--7986
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1400] [1401] [1402] [1403] [1404]
Underfull \hbox (badness 1210) in paragraph at lines 8336--8338
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1405] [1406] [1407] [1408] [1409] [1410] [1411]
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[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
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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))[]
[1413] [1414]
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[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
[1415] [1416] [1417] [1418] [1419] [1420]
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[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
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[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
[1421] [1422] [1423]
Underfull \hbox (badness 7291) in paragraph at lines 9592--9594
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of
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Underfull \hbox (badness 6944) in paragraph at lines 10070--10076
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1430] [1431] [1432] [1433]
Underfull \hbox (badness 3758) in paragraph at lines 10284--10287
[]\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
[1434] [1435] [1436]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10528--10528
[] \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
[1437]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1438]
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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 \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
Underfull \hbox (badness 10000) in paragraph at lines 10698--10701
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
fitted.values \T1/ptm/m/n/10 and
[1439] [1440] [1441]
Underfull \hbox (badness 2142) in paragraph at lines 10915--10918
[]\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 ^^@
[1442] [1443]
Underfull \hbox (badness 1708) in paragraph at lines 10996--11000
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
Underfull \hbox (badness 10000) in paragraph at lines 11038--11044
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
[1444]
Underfull \hbox (badness 1418) in paragraph at lines 11076--11081
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1445] [1446]
Underfull \hbox (badness 2635) in paragraph at lines 11209--11212
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1447] [1448]
Underfull \hbox (badness 1694) in paragraph at lines 11392--11395
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1449] [1450]
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
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[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
[1451]
Underfull \hbox (badness 10000) in paragraph at lines 11539--11543
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1452] [1453] [1454] [1455] [1456]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11861--11861
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11876 \aliasA{hat}{influence.measures}{hat}
[1457]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11936--11936
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
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[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
[1458]
Underfull \hbox (badness 1062) in paragraph at lines 12001--12006
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12018--12020
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1459] [1460] [1461] [1462]
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[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
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[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
[1463]
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[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1464] [1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 12616--12618
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
[1468]
Underfull \hbox (badness 4739) in paragraph at lines 12639--12641
[]\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
[1469]
Underfull \hbox (badness 2753) in paragraph at lines 12708--12710
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1470] [1471] [1472]
Underfull \hbox (badness 6910) in paragraph at lines 12946--12948
[]\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
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[]\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 12952--12956
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 13659--13659
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1484]
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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
[1485] [1486]
Underfull \hbox (badness 10000) in paragraph at lines 13902--13906
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
,
[1487] [1488] [1489] [1490] [1491]
Underfull \hbox (badness 1163) in paragraph at lines 14236--14244
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1492] [1493]
Underfull \hbox (badness 4518) in paragraph at lines 14356--14361
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1494] [1495] [1496]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14544--14544
[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1497] [1498] [1499] [1500] [1501]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14888--14888
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1502] [1503]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14982--14982
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1504] [1505] [1506] [1507] [1508] [1509]
Underfull \hbox (badness 2726) in paragraph at lines 15388--15391
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1510]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15482--15482
[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
[1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 16108--16108
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1521] [1522]
Underfull \hbox (badness 1490) in paragraph at lines 16246--16251
\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
[1523]
Underfull \hbox (badness 1648) in paragraph at lines 16312--16314
[]\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 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
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\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1524]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16397--16397
[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= contr.poly))[]
[1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16955--16955
[]\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[]
[1534] [1535] [1536]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17187--17187
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 17948--17948
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1549] [1550] [1551]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18111--18111
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1552]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18205--18205
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560]
Underfull \hbox (badness 1248) in paragraph at lines 18703--18706
[]\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
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[]\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
[1561]
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\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
Underfull \hbox (badness 2042) in paragraph at lines 18782--18784
[]\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
[1562] [1563]
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[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 18931--18931
[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
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[]\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 18952--18952
[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
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[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18975--18975
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
[1565]
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19010--19021
\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
[1566]
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1567] [1568] [1569]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19299--19299
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1570] [1571]
Underfull \hbox (badness 1337) in paragraph at lines 19410--19413
[]\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
[1572] [1573] [1574] [1575] [1576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19729--19729
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1577] [1578]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19817--19817
[] \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]))),[]
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[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
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[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1579]
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[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 3049) in paragraph at lines 19908--19912
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1580] [1581] [1582] [1583]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20161--20161
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 1194) in paragraph at lines 20171--20174
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1584]
Underfull \hbox (badness 1107) in paragraph at lines 20229--20231
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1585]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20284--20284
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20291--20291
[]\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)[]
[1587]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20385--20385
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1588] [1589]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20514--20514
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1590]
Underfull \hbox (badness 7740) in paragraph at lines 20577--20579
[]\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
[1591]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20625--20625
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1592]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20717--20717
[] \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 20722--20722
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603]
[1604] [1605]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21577--21577
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
equal typically[]
[1606]
Underfull \hbox (badness 6859) in paragraph at lines 21644--21651
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21655--21661
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617]
[1618]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22401--22401
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1619] [1620] [1621] [1622] [1623]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22685--22685
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22686--22686
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1624] [1625] [1626] [1627] [1628]
Underfull \hbox (badness 1337) in paragraph at lines 23012--23018
[]\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
[1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23579--23579
[] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[]
[1637] [1638]
Underfull \hbox (badness 1028) in paragraph at lines 23720--23723
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1639] [1640]
Underfull \hbox (badness 10000) in paragraph at lines 23830--23833
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1641]
Underfull \hbox (badness 7944) in paragraph at lines 23885--23887
[]\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,levels =
[1642]
Underfull \hbox (badness 7944) in paragraph at lines 23947--23949
[]\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,levels =
[1643] [1644]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24049--24049
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1645] [1646] [1647]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24269--24269
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1648]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24373--24373
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
[1649]
Underfull \hbox (badness 1033) in paragraph at lines 24416--24422
\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 24437--24440
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1650]
Underfull \hbox (badness 2134) in paragraph at lines 24506--24510
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24519--24519
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1651]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24548--24548
[]\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 24560--24560
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
[1652] [1653] [1654] [1655] [1656] [1657] [1658]
Underfull \hbox (badness 6268) in paragraph at lines 25015--25020
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/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 ,
[1659]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 25043--25043
[] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[]
[1660] [1661] [1662]
Underfull \hbox (badness 1867) in paragraph at lines 25220--25222
[]\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 25235--25239
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback =
use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25235--25239
\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 25271--25271
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
[1663] [1664] [1665]
Underfull \hbox (badness 2495) in paragraph at lines 25461--25470
[]\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 .
[1666]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25543--25543
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
[1667]
Underfull \hbox (badness 1412) in paragraph at lines 25550--25552
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1668]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25637--25637
[]\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 25662--25662
[]\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 25665--25665
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1669] [1670] [1671]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 25889--25889
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 25893--25899
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1672]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25939--25939
[]\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 25960--25960
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1673]
Underfull \hbox (badness 1019) in paragraph at lines 26022--26027
\T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow
\T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value
[1674] [1675]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26152--26152
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1676] [1677] [1678] [1679] [1680] [1681]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26531--26531
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1682] [1683]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26712--26712
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
[1684]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26718--26718
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean) f
or when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26727--26727
[]\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 26728--26728
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
[1685]
Underfull \hbox (badness 2922) in paragraph at lines 26797--26802
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26834--26834
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
[1686]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26837--26837
[] \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 26846--26846
[] \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 26847--26847
[] \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 26851--26851
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1687]
Underfull \hbox (badness 3240) in paragraph at lines 26905--26908
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26926--26926
[] \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 26929--26929
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1688]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27012--27012
[] \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 27016--27016
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
[1689]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 27026--27026
[] \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 27031--27031
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
Underfull \hbox (badness 2922) in paragraph at lines 27067--27073
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1690]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27089--27089
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27105--27105
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1691] [1692]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 27219--27219
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1693]
Underfull \hbox (badness 2922) in paragraph at lines 27281--27286
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27319--27319
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1694]
Underfull \hbox (badness 2922) in paragraph at lines 27368--27373
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1695]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27399--27399
[]\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 27433--27438
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1696]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27458--27458
[]\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 27462--27462
[]\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 27482--27482
[] \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 27492--27492
[] \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[]
[1697]
Underfull \hbox (badness 2922) in paragraph at lines 27527--27532
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27549--27549
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1698]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27567--27567
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
Underfull \hbox (badness 6493) in paragraph at lines 27619--27624
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1699]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27647--27647
[]\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 27650--27650
[]\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 27653--27653
[]\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 27656--27656
[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
[1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710]
[1711] [1712] [1713]
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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/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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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/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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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/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 giv
en 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-
e-sis, must be one of
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[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i
-tive nu-meric tol-er-ance, used in
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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/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
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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 "")[]
[1770]) (./stats4-pkg.tex
Chapter 11.
[1771] [1772] [1773]
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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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l.503 ...Package \pkg{stats4}}{show.Rdash.methods}
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(./tcltk-pkg.tex [1782]
Chapter 12.
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
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-ing
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-cept
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1802]) (./tools-pkg.tex
Chapter 13.
[1803]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1804]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
which will be eval-u-ated via
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
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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/1
0 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/1
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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-gine
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, ...)[]
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
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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
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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
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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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tm/m/n/10 and
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[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
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[] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[]
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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","Enhances")\T1/ptm/
m/n/10 .
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
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[]\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[]
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[] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[]
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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
[1838]
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[]\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[]
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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","Enhances")\T1/ptm/
m/n/10 .
[1839]
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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/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[]
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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"),[]
[1844]
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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-to
r 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 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
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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 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
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[] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
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[] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
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[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright,
bugs)
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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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/p
tm/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
[1871] [1872] [1873] [1874]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4730--4730
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4731--4731
[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[]
Underfull \hbox (badness 3240) in paragraph at lines 4743--4746
[]\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 4747--4757
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4782--4788
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4782--4788
\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 ',
[1875]
Underfull \hbox (badness 1571) in paragraph at lines 4810--4814
[]\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 4836--4841
\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
[1876] [1877] [1878]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1879] [1880] [1881] [1882]
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[]
[1883]
Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383
\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1884]
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
[1885]
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"))),[]
[1886] [1887]
Underfull \hbox (badness 1946) in paragraph at lines 626--630
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1888]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 676--676
[]\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"),
Overfull \hbox (6.78088pt too wide) in paragraph at lines 682--682
[]\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 683--683
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 684--684
[]\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 685--685
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Underfull \hbox (badness 10000) in paragraph at lines 719--725
[]\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 719--725
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1889] [1890]
Underfull \hbox (badness 4505) in paragraph at lines 855--861
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1891] [1892] [1893]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1029--1029
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1894]
Underfull \hbox (badness 1748) in paragraph at lines 1094--1102
[]\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-
Underfull \hbox (badness 1661) in paragraph at lines 1094--1102
\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 1094--1102
\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 1106--1108
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1895]
Underfull \hbox (badness 10000) in paragraph at lines 1214--1217
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1896]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1297--1297
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1799--1799
[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1834--1834
[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1905] [1906]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1980--1980
[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1907] [1908]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2132--2132
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1909]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2184--2184
[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1910] [1911] [1912]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2353--2353
[] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2376--2376
[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[1913] [1914]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2496--2496
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1915]
Underfull \hbox (badness 1082) in paragraph at lines 2570--2574
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2575 ... the Clipboard in MS Windows}{clipboard}
Underfull \hbox (badness 1163) in paragraph at lines 2606--2608
[]\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 .
[1916] [1917]
Underfull \hbox (badness 10000) in paragraph at lines 2694--2696
[]\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
[1918] [1919] [1920]
Underfull \hbox (badness 10000) in paragraph at lines 2911--2913
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1921] [1922] [1923] [1924]
Underfull \hbox (badness 1762) in paragraph at lines 3205--3208
[]\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 =
[1925]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3298--3298
[]\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 '[]
[1926]
Underfull \hbox (badness 2452) in paragraph at lines 3374--3377
[]\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
[1927] [1928] [1929] [1930] [1931] [1932]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3783--3783
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[1933] [1934]
Underfull \hbox (badness 10000) in paragraph at lines 3867--3871
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is
op-tional on Win-dows: use
Underfull \hbox (badness 1072) in paragraph at lines 3924--3932
[]\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
[1935]
Underfull \hbox (badness 1231) in paragraph at lines 4001--4013
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 4015--4020
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method =
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 4015--4020
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
of
Underfull \hbox (badness 1331) in paragraph at lines 4015--4020
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
brack-ets are op-tional. See
[1936] [1937]
Underfull \hbox (badness 4660) in paragraph at lines 4135--4138
\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
Underfull \hbox (badness 10000) in paragraph at lines 4159--4161
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1938] [1939] [1940]
Underfull \hbox (badness 1565) in paragraph at lines 4344--4348
[]\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
[1941]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4427--4427
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[1942]
Underfull \hbox (badness 1931) in paragraph at lines 4462--4469
[]\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)
[1943] [1944] [1945] [1946] [1947]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4786--4786
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.4857 ...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.4857 ...mat Unordered and Ordered Lists}{format}
[1949] [1950] [1951]
[1952] [1953] [1954] [1955] [1956]
Underfull \hbox (badness 1622) in paragraph at lines 5376--5380
[]\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
[1957] [1958] [1959] [1960] [1961]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 5698--5698
[]\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 5710--5710
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
[1962] [1963]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5843--5843
[] \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 5844--5844
[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
[1964] [1965] [1966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6054--6054
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1967]
Underfull \hbox (badness 10000) in paragraph at lines 6138--6140
[]\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
[1968]
Underfull \hbox (badness 1502) in paragraph at lines 6187--6192
[]\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 6187--6192
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1969] [1970]
Underfull \hbox (badness 10000) in paragraph at lines 6360--6369
[]\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 6360--6369
\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
[1971]
Underfull \hbox (badness 2150) in paragraph at lines 6424--6427
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6440--6443
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search
database for sub-se-quent use by
[1972] [1973]
Underfull \hbox (badness 3118) in paragraph at lines 6562--6564
[]\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
[1974] [1975]
Underfull \hbox (badness 5091) in paragraph at lines 6736--6738
[]\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
[1976]
Underfull \hbox (badness 5331) in paragraph at lines 6752--6758
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6752--6758
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6752--6758
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6766--6773
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
Underfull \hbox (badness 1270) in paragraph at lines 6781--6791
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
[1977]
Underfull \hbox (badness 10000) in paragraph at lines 6824--6827
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be
Underfull \hbox (badness 10000) in paragraph at lines 6824--6827
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
Underfull \hbox (badness 1424) in paragraph at lines 6832--6835
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 6889--6893
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
[1978]
Underfull \hbox (badness 2376) in paragraph at lines 6903--6910
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 6903--6910
\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 6903--6910
\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 6911--6914
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1979]
Underfull \hbox (badness 1314) in paragraph at lines 6990--6997
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
Underfull \hbox (badness 10000) in paragraph at lines 7047--7052
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7070--7070
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
[1980]
Underfull \hbox (badness 5133) in paragraph at lines 7106--7110
[]\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 7120--7123
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1981]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7167--7167
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1982] [1983]
Underfull \hbox (badness 4132) in paragraph at lines 7287--7289
[]\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
[1984] [1985] [1986]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7454--7454
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1987] [1988]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7597--7597
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1989]
Underfull \hbox (badness 10000) in paragraph at lines 7637--7639
[]\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
[1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 7825--7827
[]\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 7830--7832
[]\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
[1992] [1993] [1994] [1995]
Underfull \hbox (badness 1859) in paragraph at lines 8058--8061
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1996]
Underfull \hbox (badness 1655) in paragraph at lines 8152--8155
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8163--8163
[]\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 8171--8171
[]\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):[]
[1997]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8179--8179
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1998]
Underfull \hbox (badness 1917) in paragraph at lines 8266--8268
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[1999] [2000] [2001] [2002]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8538--8538
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8539--8539
[] \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 8540--8540
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[2003]
Underfull \hbox (badness 10000) in paragraph at lines 8568--8570
[]\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 8582--8584
[]\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 8590--8595
[]\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,
[2004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8636--8636
[] \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 8637--8637
[] \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[]
[2005] [2006]
Underfull \hbox (badness 10000) in paragraph at lines 8766--8771
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8766--8771
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8766--8771
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8773--8776
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[2007]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8889--8889
[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8890--8890
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[2008] [2009] [2010]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9061--9061
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[2011]
Underfull \hbox (badness 1789) in paragraph at lines 9192--9194
[]\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
[2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020]
Underfull \hbox (badness 5203) in paragraph at lines 9765--9768
[]\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
[2021] [2022]
Underfull \hbox (badness 1394) in paragraph at lines 9991--9998
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
, try-ing to com-plete
[2023]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10015--10015
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[2024] [2025]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10176--10176
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[2026] [2027] [2028]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10357--10357
[]\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[]
[2029]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10443--10443
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10446--10446
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10451--10451
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2030]
Underfull \hbox (badness 2027) in paragraph at lines 10523--10526
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[2031] [2032] [2033] [2034]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10795--10795
[]\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 10796--10796
[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
Underfull \hbox (badness 10000) in paragraph at lines 10803--10808
[]\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 10803--10808
\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 10803--10808
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2035] [2036] [2037]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11036--11036
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2038] [2039] [2040] [2041] [2042]
Underfull \hbox (badness 10000) in paragraph at lines 11297--11301
\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 11315--11315
[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11320--11320
[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[2043] [2044]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11453--11453
[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 11454--11454
[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
[2045] [2046]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11589--11589
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[2047]
Underfull \hbox (badness 1917) in paragraph at lines 11713--11716
[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
Underfull \hbox (badness 4328) in paragraph at lines 11713--11716
\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
[2048]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 11736--11736
[]\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 '[]
[2049]
Underfull \hbox (badness 10000) in paragraph at lines 11799--11801
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
[2050]
Underfull \hbox (badness 6725) in paragraph at lines 11849--11858
\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/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 11849--11858
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 11849--11858
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2051]
Underfull \hbox (badness 3646) in paragraph at lines 11975--11977
[][][]$\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 /
[2052]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12013--12013
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[2053] [2054] [2055]
Underfull \hbox (badness 10000) in paragraph at lines 12194--12198
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12225--12231
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2056] [2057]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12401--12401
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[2058]
Underfull \hbox (badness 1009) in paragraph at lines 12419--12431
[]\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 12459--12461
[]\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
[2059]
Underfull \hbox (badness 1043) in paragraph at lines 12502--12507
[]\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
[2060] [2061] [2062] [2063]
Underfull \hbox (badness 1888) in paragraph at lines 12795--12798
[]\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 12812--12815
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2064]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12853--12853
[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
[2065]
Underfull \hbox (badness 2158) in paragraph at lines 12908--12911
[]\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 12956--12956
[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
[2066] [2067] [2068]
Underfull \hbox (badness 2302) in paragraph at lines 13113--13115
[]\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
[2069]
Underfull \hbox (badness 3333) in paragraph at lines 13220--13222
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2070] [2071] [2072]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 13387--13387
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
Underfull \hbox (badness 2012) in paragraph at lines 13411--13416
[]\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 have
Underfull \hbox (badness 5970) in paragraph at lines 13420--13423
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13420--13423
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2073]
Underfull \hbox (badness 1442) in paragraph at lines 13447--13451
[]\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault,
de-ter-min-ing the \T1/pcr/m/n/10 nlines \T1/ptm/m/n/10 ar-gu-ment to
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13479--13479
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2074]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13517--13517
[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13519--13519
[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[2075] [2076]
Underfull \hbox (badness 10000) in paragraph at lines 13687--13689
[]\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
[2077] [2078] [2079]
Underfull \hbox (badness 6300) in paragraph at lines 13844--13851
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 13844--13851
\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
[2080] [2081]
Underfull \hbox (badness 2020) in paragraph at lines 14013--14029
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 14013--14029
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2082] [2083]
Underfull \hbox (badness 5022) in paragraph at lines 14153--14157
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 14160--14163
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 14160--14163
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2084] [2085] [2086]
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[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
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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
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.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 and \T
1/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 ,
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\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \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
[2093]
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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 av
ailable.packages(contriburl =
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\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
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
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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.packages[]
[][]\T1/ptm/m/n/10 ,
[2094]
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[]\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt")
[2095] [2096] [2097]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2098]
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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:[]
[2099]
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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)))[]
[2100] [2101]
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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
[2102]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2103] [2104]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2105]
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[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15664--15666
[]\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 =
[2106] [2107] [2108]) [2109] [2110] (./KernSmooth-pkg.tex
Chapter 15.
[2111]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2112] [2113] [2114] [2115] [2116]
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[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2117] [2118] [2119] [2120]) (./MASS-pkg.tex
Chapter 16.
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131]
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[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
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[2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
[2154]
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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"),[]
[2155] [2156] [2157] [2158]
Underfull \hbox (badness 6559) in paragraph at lines 2698--2701
[]\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
[2159] [2160] [2161]
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\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2868--2873
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\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 ,
[2162] [2163]
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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
[2164] [2165] [2166]
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[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
[2167]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178]
[2179]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2180] [2181] [2182] [2183] [2184] [2185] [2186]
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[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[2187] [2188] [2189]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
[2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200]
[2201] [2202] [2203]
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2204]
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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")
[2205] [2206]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6123 ...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.6123 ...sical N, P, K Factorial Experiment}{npk}
[2207]
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[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space.
That is
[2208] [2209] [2210] [2211]
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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)))[]
[2213]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2214] [2215] [2216] [2217] [2218] [2219]
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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"))[]
[2220]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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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 ) =
[2221]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2222] [2223]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2224] [2225]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2226]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2227] [2228] [2229] [2230] [2231] [2232]
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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
[2233] [2234]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8096--8096
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
Underfull \hbox (badness 1590) in paragraph at lines 8120--8124
[]\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
[2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245]
[2246] [2247] [2248] [2249] [2250] [2251] [2252] [2253] [2254]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9499--9499
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2255]
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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 ,
Underfull \hbox (badness 1158) in paragraph at lines 9626--9629
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2256]
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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)[]
[2257] [2258] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267]
[2268] [2269]) (./Matrix-pkg.tex [2270]
Chapter 17.
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[]\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
[2271]
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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
[2272]
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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
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\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2273]
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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
[2274] [2275]
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[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2276]
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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/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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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)[]
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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)],[]
[2277] [2278]
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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}"}.[]
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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)[]
[2279]
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[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2280] [2281] [2282]
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[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2283] [2284]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
[2285pdfTeX warning (ext4):
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2286]
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[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2287]
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[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
Underfull \hbox (badness 2277) in paragraph at lines 1389--1392
[]\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
[2288]
Underfull \hbox (badness 1609) in paragraph at lines 1436--1440
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2289]
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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[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1485--1485
[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
[2290]
Underfull \hbox (badness 10000) in paragraph at lines 1532--1539
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1532--1539
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1567--1571
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1583--1589
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2291]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1624 ... 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.1624 ... 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.1625 \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.1646 \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.1657 \aliasA{rowSums}{colSums}{rowSums}
[2292]
Underfull \hbox (badness 2922) in paragraph at lines 1711--1715
[]\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 1711--1715
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1722--1725
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2293] [2294]
Underfull \hbox (badness 3547) in paragraph at lines 1876--1879
[]\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
[2295] [2296] [2297] [2298] [2299]
Underfull \hbox (badness 1484) in paragraph at lines 2238--2240
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2300]
Underfull \hbox (badness 7379) in paragraph at lines 2334--2336
[]\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
[2301] [2302] [2303]
Underfull \hbox (badness 4846) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2615--2619
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2622--2625
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2304]
Underfull \hbox (badness 2689) in paragraph at lines 2678--2680
[]\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 2682--2687
[]\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 2682--2687
[][]\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
[2305]
Underfull \hbox (badness 1097) in paragraph at lines 2705--2708
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2718--2723
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2306]
Underfull \hbox (badness 3646) in paragraph at lines 2957--2960
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2989--2991
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 2992--2996
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 3001--3007
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2307]
Underfull \hbox (badness 10000) in paragraph at lines 3008--3012
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3018--3022
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2308] [2309]
Underfull \hbox (badness 10000) in paragraph at lines 3202--3204
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3249--3251
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2310]
Underfull \hbox (badness 2469) in paragraph at lines 3369--3372
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
, via
[2311] [2312]
Underfull \hbox (badness 10000) in paragraph at lines 3534--3538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3534--3538
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2313]
Underfull \hbox (badness 2285) in paragraph at lines 3584--3587
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2314] [2315]
Underfull \hbox (badness 10000) in paragraph at lines 3731--3736
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3731--3736
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3743--3746
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 :
if \T1/pcr/m/n/10 uplo ==
[2316]
Underfull \hbox (badness 10000) in paragraph at lines 3819--3821
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2317] [2318] [2319]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4029--4029
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 4097--4101
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
[2320]
Underfull \hbox (badness 10000) in paragraph at lines 4106--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4106--4109
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4111--4115
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
: the
[2321] [2322]
Underfull \hbox (badness 3158) in paragraph at lines 4294--4298
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2323] [2324] [2325] [2326]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4533--4533
[] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[]
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4536--4536
[] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4540--4540
[]\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 4543--4543
[]\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():[]
[2327] [2328] [2329] [2330]
Underfull \hbox (badness 10000) in paragraph at lines 4855--4860
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2331]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4936--4936
[]\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 4938--4938
[] \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 4942--4942
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2332]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4949--4949
[] \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 '[]
[2333] [2334]
Underfull \hbox (badness 4120) in paragraph at lines 5093--5096
[]\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 (15.18042pt too wide) in paragraph at lines 5130--5130
[]\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 5136--5136
[] \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 5137--5137
[] \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 5140--5140
[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5142--5142
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
[2335]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5149--5149
[]\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[]
[2336]
Underfull \hbox (badness 1817) in paragraph at lines 5241--5250
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 10000) in paragraph at lines 5283--5285
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5285--5288
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2337]
Underfull \hbox (badness 4765) in paragraph at lines 5316--5319
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2338]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5376--5376
[] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[]
[2339] [2340] [2341]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5634--5634
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[]
[2342]
Underfull \hbox (badness 10000) in paragraph at lines 5715--5718
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5726--5726
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2343]
Underfull \hbox (badness 1622) in paragraph at lines 5763--5768
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
\T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5763--5768
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2344]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5824--5824
[]\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 5825--5825
[] \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 5832--5832
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2345]
Underfull \hbox (badness 1062) in paragraph at lines 5961--5964
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2346]
Underfull \hbox (badness 6063) in paragraph at lines 5990--5993
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2347]
Underfull \hbox (badness 2635) in paragraph at lines 6102--6107
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6102--6107
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 6110--6113
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 6220--6230
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6220--6230
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2349]
Underfull \hbox (badness 3179) in paragraph at lines 6302--6305
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2350]
Underfull \hbox (badness 10000) in paragraph at lines 6400--6403
[]\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.,
[2351]
Underfull \hbox (badness 10000) in paragraph at lines 6475--6478
[]\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.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6491--6491
[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2352]
Underfull \hbox (badness 2443) in paragraph at lines 6530--6536
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6530--6536
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6551--6554
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2353]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6621--6621
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2354] [2355]
Underfull \hbox (badness 6268) in paragraph at lines 6757--6760
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
Underfull \hbox (badness 5036) in paragraph at lines 6781--6785
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
. How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6781--6785
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2356] [2357]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again>
\relax
l.6874 \aliasA{det}{Matrix-class}{det}
Underfull \hbox (badness 10000) in paragraph at lines 6977--6980
Underfull \hbox (badness 10000) in paragraph at lines 6987--6989
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2358]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.7050 ...*\%}{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.7158 ...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.7258 ...tcrossprod}{matrix-products}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 7356--7362
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2359] [2360pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7418 \end{Details}
pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7418 \end{Details}
]
Underfull \hbox (badness 10000) in paragraph at lines 7429--7432
[]\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 1199) in paragraph at lines 7429--7432
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 7432--7437
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 1371) in paragraph at lines 7432--7437
\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
Underfull \hbox (badness 1502) in paragraph at lines 7437--7441
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
Underfull \hbox (badness 10000) in paragraph at lines 7437--7441
\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
"dgeMatrix")\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 2837) in paragraph at lines 7447--7448
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2361] [2362]
Underfull \hbox (badness 1009) in paragraph at lines 7583--7585
[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
$\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
Underfull \hbox (badness 1062) in paragraph at lines 7628--7631
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2363]
Underfull \hbox (badness 6063) in paragraph at lines 7662--7665
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2364]
Underfull \hbox (badness 10000) in paragraph at lines 7714--7716
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2365] [2366]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7853--7853
[]\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 [2367]
Underfull \hbox (badness 2635) in paragraph at lines 7918--7923
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7918--7923
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7926--7929
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2368]
Underfull \hbox (badness 3482) in paragraph at lines 8000--8006
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
that these co-er-cions
[2369]
Underfull \hbox (badness 1867) in paragraph at lines 8120--8122
[]\T1/ptm/m/n/10 fast sim-
[2370]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8160 \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.8160 \HeaderA{norm}{Matrix Norms}{norm}
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8247--8247
[]\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 8248--8248
[]\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 8249--8249
[]\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 8362--8372
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2372]
Underfull \hbox (badness 3179) in paragraph at lines 8433--8436
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2373]
Underfull \hbox (badness 10000) in paragraph at lines 8523--8526
[]\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.,
[2374]
Underfull \hbox (badness 10000) in paragraph at lines 8599--8602
[]\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.,
[2375]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8615--8615
[]\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
Overfull \vbox (41.60564pt too high) has occurred while \output is active
[2376]
Underfull \hbox (badness 10000) in paragraph at lines 8725--8727
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
sig-na-tures (use
Underfull \hbox (badness 6493) in paragraph at lines 8727--8730
[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
Underfull \hbox (badness 6428) in paragraph at lines 8733--8740
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2377] [2378]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8826--8826
[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829
[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8831--8831
[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8835--8835
[]\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,[]
Underfull \hbox (badness 3989) in paragraph at lines 8861--8871
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8861--8871
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2379] [2380]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.8962 \aliasA{qr}{qr-methods}{qr}
[2381]
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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![]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9046--9046
[]\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 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[]
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[]\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[]
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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
Underfull \hbox (badness 10000) in paragraph at lines 9145--9148
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2383]
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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"[]
[2384]
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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![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.9258 ... the Reciprocal Condition Number}{rcond}
[2385] [2386]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9371--9371
[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2387] [2388]
Underfull \hbox (badness 10000) in paragraph at lines 9556--9558
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
via one di-men-sional
Underfull \hbox (badness 1325) in paragraph at lines 9562--9570
\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
not
[2389] [2390]
Underfull \hbox (badness 1558) in paragraph at lines 9707--9710
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2391]
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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:[]
[2392]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9835 \aliasA{solve}{solve-methods}{solve}
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[] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[]
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[] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[]
[2393]
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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
Underfull \hbox (badness 10000) in paragraph at lines 9989--9992
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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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 : Checks
if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
[2394]
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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
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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
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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[][][]\T
1/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[]
[2395]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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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 con-t
rasts to be ap-plied to the
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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
[2396]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
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[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
\T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
be of-
[2397]
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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),[]
[2398] [2399]
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[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
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[] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij =
FALSE)[]
[2400]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2401]
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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[]
[2402]
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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)[]
[2403]
Underfull \hbox (badness 10000) in paragraph at lines 10740--10748
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
[2404]
Underfull \hbox (badness 10000) in paragraph at lines 10791--10795
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.10831 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2405] [2406]
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[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/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[]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
[2407]
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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 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2408]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2409]
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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-struc
-tion of sparse vec-tors (apart from
[2410] [2411]
Underfull \hbox (badness 2698) in paragraph at lines 11382--11388
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2412]
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[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
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[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11493--11498
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11501--11506
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2413]
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[]\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.,
[2414] [2415]
Underfull \hbox (badness 6641) in paragraph at lines 11659--11662
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
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[]\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
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\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
[2416]
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[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2417] [2418] [2419]
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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
[2420]
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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)[]
[2421] [2422]
Underfull \hbox (badness 6910) in paragraph at lines 12296--12298
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2423] [2424] [2425]) (./boot-pkg.tex [2426]
Chapter 18.
[2427] [2428] [2429] [2430] [2431] [2432] [2433]
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2434]
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[]\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
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[]\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-
[2435] [2436] [2437]
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[]\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.
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[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2438]
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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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[2440]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
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\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply
\T1/pcr/m/n/10 "all"
[2441]
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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
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\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
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2442] [2443] [2444] [2445]
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-
[2446] [2447] [2448] [2449] [2450]
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),
[2451] [2452] [2453]
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[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2455]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2456] [2457] [2458]
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[]\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
[2459]
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\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
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 ,
[2460] [2461]
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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/10 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/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2462] [2463] [2464] [2465] [2466]
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[]\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,[]
[2467] [2468] [2469]
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[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2470]
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[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2471] [2472] [2473]
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
[2474] [2475] [2476] [2477] [2478] [2479] [2480]
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)[]
[2481] [2482]
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])[]
[2483] [2484] [2485]
Underfull \hbox (badness 10000) in paragraph at lines 4190--4192
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2486]
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
[2487] [2488]
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-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2489] [2490] [2491] [2492] [2493] [2494] [2495] [2496] [2497]
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
[2498] [2499] [2500] [2501]
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
[2502]
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])[]
[2503] [2504] [2505] [2506] [2507] [2508] [2509] [2510]
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][]
[2511]
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 t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2512]
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 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2513] [2514] [2515] [2516]
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).
[2517] [2518]
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[]
[2519] [2520] [2521]
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
[2522] [2523]
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),[]
[2524] [2525] [2526] [2527] [2528] [2529] [2530] [2531]) (./class-pkg.tex
[2532]
Chapter 19.
[2533] [2534] [2535] [2536] [2537] [2538] [2539] [2540] [2541] [2542] [2543]
[2544] [2545] [2546] [2547] [2548]) (./cluster-pkg.tex
Chapter 20.
[2549]
Underfull \hbox (badness 1655) in paragraph at lines 134--143
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 134--143
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 134--143
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 134--143
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2550] [2551]
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]))[]
[2552] [2553]
Underfull \vbox (badness 10000) has occurred while \output is active [2554]
[2555]
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,
...)[]
[2556] [2557]
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)[]
[2558]
Underfull \hbox (badness 3078) in paragraph at lines 689--692
[]\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
[2559] [2560]
Underfull \hbox (badness 2941) in paragraph at lines 780--783
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 818--818
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2561]
Underfull \hbox (badness 10000) in paragraph at lines 865--867
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2562]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 930--930
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2563]
Underfull \hbox (badness 4872) in paragraph at lines 976--978
[]\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 990--994
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2564]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1104--1104
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2565]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1121--1121
[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1159--1159
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
[2566]
Underfull \hbox (badness 4144) in paragraph at lines 1191--1195
[]\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
[2567]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1267--1267
[] \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 1273--1273
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2568] [2569]
Underfull \hbox (badness 10000) in paragraph at lines 1412--1417
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 1460--1463
[2570]
Underfull \hbox (badness 10000) in paragraph at lines 1477--1481
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1501--1501
[]\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 1511--1511
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2571]
Underfull \hbox (badness 5741) in paragraph at lines 1551--1554
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2572]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1620--1620
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2573]
Underfull \hbox (badness 1540) in paragraph at lines 1737--1745
\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 =
[2574] [2575]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1828--1828
[]\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 1847--1847
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2576] [2577] [2578] [2579]
Underfull \hbox (badness 10000) in paragraph at lines 2166--2169
[2580]
Underfull \hbox (badness 3179) in paragraph at lines 2180--2186
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2581] [2582]
Underfull \hbox (badness 10000) in paragraph at lines 2338--2341
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2583]
Underfull \hbox (badness 1292) in paragraph at lines 2406--2409
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
Underfull \hbox (badness 6675) in paragraph at lines 2415--2417
[]\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 2438--2441
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2584] [2585] [2586] [2587]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2654--2654
[]\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 ):[]
[2588] [2589] [2590]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2923--2923
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2591] [2592]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3026--3026
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2593] [2594] [2595]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3222--3222
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3223--3223
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2596]
Underfull \hbox (badness 10000) in paragraph at lines 3290--3293
[]\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
[2597]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3340--3340
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3341--3341
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2598] [2599] [2600]
Underfull \hbox (badness 10000) in paragraph at lines 3526--3529
[]\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
[2601]
Underfull \hbox (badness 10000) in paragraph at lines 3589--3594
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2602]
Underfull \hbox (badness 3884) in paragraph at lines 3651--3656
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3663--3666
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2603] [2604] [2605]
Underfull \hbox (badness 10000) in paragraph at lines 3848--3851
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3879--3882
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2606]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3932--3932
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3943--3945
[]\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
[2607] [2608] [2609] [2610]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4136--4136
[] \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 4138--4138
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2611] [2612]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4276--4276
[]\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 4285--4285
[] \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 4287--4287
[] \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 4290--4290
[]\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 4292--4292
[] \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 4299--4299
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2613] [2614] [2615] [2616] [2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 4672--4678
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4688--4690
[]\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
[2619]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4701--4701
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
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[]\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[]
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[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
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[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2620]) (./codetools-pkg.tex
Chapter 21.
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[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
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[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
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[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2621]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2622]
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[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2623] [2624] [2625]) (./foreign-pkg.tex [2626]
Chapter 22.
[2627]
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
[2628] [2629]
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 ,
[2630]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2631] [2632] [2633]
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[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2634]
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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-
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\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named
to
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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10
,
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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 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2635]
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[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 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
[2636]
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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,[]
[2637]
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[]\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="")[]
[2638] [2639]
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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])[]
[2640] [2641]
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)
[2642]
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[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2643] [2644]
Underfull \hbox (badness 10000) in paragraph at lines 1076--1077
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
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[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2645] [2646]
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 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2647]
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 side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2648]) (./lattice-pkg.tex
Chapter 23.
[2649]
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 /
[2650] [2651]
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"),[]
[2652]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
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[] \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"),[]
[2653] [2654] [2655] [2656]
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
[2657] [2658] [2659] [2660]
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[]\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.
[2661]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2662] [2663]
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
[2664] [2665] [2666]
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 ,
[2667]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2668]
Underfull \vbox (badness 10000) has occurred while \output is active [2669]
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
[2670]
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\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
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
[2671] [2672] [2673] [2674]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
[2675]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2676] [2677] [2678]
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"),[]
[2679] [2680] [2681] [2682] [2683]
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"),[]
[2684] [2685]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2686]
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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 2888--2892
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2894--2896
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
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[]\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,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2970--2974
[]\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
[2687] [2688]
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[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
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[] \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 3075--3075
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
[2689]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
Underfull \hbox (badness 2913) in paragraph at lines 3156--3163
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3156--3163
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2690] [2691] [2692] [2693]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3444 \aliasA{parallel}{B\_08\_splom}{parallel}
[2694]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3509--3509
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2695] [2696] [2697] [2698] [2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3845--3845
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2700]
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[]\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
[2701] [2702]
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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
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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
[2703]
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\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4183--4187
\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
[2704] [2705]
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
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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 ,
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\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
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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 f
or \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 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
[2706]
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4325--4327
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2707] [2708] [2709] [2710] [2711]
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[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2712] [2713]
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[]\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 .
[2714] [2715]
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[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2716] [2717] [2718] [2719] [2720] [2721]
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[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
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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],[]
[2722]
Underfull \hbox (badness 10000) in paragraph at lines 5501--5504
[]\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 5501--5504
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2723]
Underfull \hbox (badness 1635) in paragraph at lines 5527--5532
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2724]
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[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2725]
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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"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5696--5696
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5699--5699
[] \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 5707--5707
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5708--5708
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5709--5709
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5710--5710
[] \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
[2726] [2727]
Underfull \hbox (badness 2538) in paragraph at lines 5863--5867
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5874--5881
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5874--5881
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2728] [2729]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6031
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2730] [2731]
Underfull \hbox (badness 4242) in paragraph at lines 6174--6179
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2732] [2733]
Underfull \hbox (badness 3601) in paragraph at lines 6290--6295
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6290--6295
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2734]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6377--6377
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2735] [2736]
Underfull \hbox (badness 1888) in paragraph at lines 6509--6516
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2737]
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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 6566--6569
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2738] [2739] [2740] [2741] [2742] [2743]
Underfull \hbox (badness 1320) in paragraph at lines 6972--6979
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6972--6979
\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
[2744]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7042--7042
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2745]
Underfull \hbox (badness 10000) in paragraph at lines 7072--7076
[]\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 7072--7076
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 7177--7180
\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
[2747] [2748]
Underfull \hbox (badness 2012) in paragraph at lines 7343--7346
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2749]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7389--7389
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2750] [2751]
Underfull \hbox (badness 2644) in paragraph at lines 7530--7534
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7543--7546
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
[2752]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7613--7613
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7623--7623
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2753]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7689--7689
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2754] [2755] [2756]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7874--7874
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2757]
Underfull \hbox (badness 1436) in paragraph at lines 7929--7935
[]\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
[2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765]
Underfull \hbox (badness 10000) in paragraph at lines 8487--8490
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8487--8490
\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
[2766] [2767]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8662--8662
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8663--8663
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8675--8675
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2768]
Underfull \hbox (badness 3118) in paragraph at lines 8694--8697
[]\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
[2769]
Underfull \hbox (badness 1515) in paragraph at lines 8770--8774
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2770]
Underfull \hbox (badness 6316) in paragraph at lines 8876--8881
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2771] [2772]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8983--8983
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2773] [2774]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9122--9122
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2775]
Overfull \hbox (42.94879pt too wide) in paragraph at lines 9181--9185
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
Overfull \hbox (50.63074pt too wide) in paragraph at lines 9181--9185
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2776] [2777] [2778] [2779] [2780] [2781] [2782]
Underfull \hbox (badness 7238) in paragraph at lines 9639--9643
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9639--9643
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2783] [2784] [2785]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9870 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2786] [2787] [2788]
Underfull \hbox (badness 10000) in paragraph at lines 10032--10037
\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 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10105--10105
[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2789] [2790]) (./mgcv-pkg.tex
Chapter 24.
[2791] [2792]
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,[]
[2793]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 165--165
[] \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
Underfull \hbox (badness 1043) in paragraph at lines 209--214
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2794] [2795] [2796] [2797]
Underfull \hbox (badness 10000) in paragraph at lines 378--385
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 378--385
[][]\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 378--385
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2798]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 421--421
[]\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)+[]
[2799] [2800] [2801]
Underfull \hbox (badness 2922) in paragraph at lines 633--634
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2802] [2803]
Underfull \hbox (badness 2205) in paragraph at lines 703--704
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-i
ng evi-ron-ment vari-able
[2804] [2805]
Underfull \hbox (badness 1158) in paragraph at lines 813--815
[]\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
[2806]
Underfull \hbox (badness 1259) in paragraph at lines 876--877
[]\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).
[2807]
Underfull \vbox (badness 10000) has occurred while \output is active [2808]
[2809] [2810] [2811] [2812]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1224--1224
[]\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 1225--1225
[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1231--1231
[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1238--1238
[]\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
this stratum...[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1240--1240
[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242
[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
[2813]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1273--1273
[]\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)[]
[2814]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1334--1334
[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
[2815]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1345--1345
[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1379--1379
[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
[2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1882--1882
[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2824] [2825] [2826] [2827] [2828] [2829] [2830]
Underfull \hbox (badness 1052) in paragraph at lines 2270--2278
\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2287--2287
[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
Underfull \hbox (badness 1728) in paragraph at lines 2299--2302
[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
Underfull \hbox (badness 1142) in paragraph at lines 2312--2316
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2831]
Underfull \hbox (badness 1043) in paragraph at lines 2338--2343
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2832] [2833] [2834]
Underfull \hbox (badness 1043) in paragraph at lines 2503--2509
\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
[2835]
Underfull \hbox (badness 10000) in paragraph at lines 2639--2645
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
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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 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
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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/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
[2854]
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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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[2857]
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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)+[]
[2866] [2867]
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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,
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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
[2870]
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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-genc
e fail-ures, con-sider mod-i-fy-ing
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[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
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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
[2879] [2880] [2881] [2882] [2883] [2884] [2885]
Underfull \hbox (badness 6708) in paragraph at lines 5604--5605
[]\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
[2886]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
[2887]
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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])[]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
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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[]
[2889] [2890] [2891] [2892] [2893]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
[2894]
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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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[2899]
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[]\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2)
[2900]
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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)
[2901] [2902] [2903] [2904]
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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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Underfull \hbox (badness 1242) in paragraph at lines 7436--7437
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2920]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
[2921]
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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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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8825--8828
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2941]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
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\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
be
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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,[]
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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
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[2951]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[]
[2952]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para-
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\T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c
luded terms,
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
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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[]
[2959]
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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
[2960]
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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
[2961]
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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-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2962] [2963]
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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,
[2964] [2965] [2966] [2967]
Underfull \hbox (badness 1946) in paragraph at lines 10417--10424
[]\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: s
ee
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
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\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2968]
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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)[]
[2969]
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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 ,
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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)
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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,[]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2981]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
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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
[2984] [2985]
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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 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
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\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
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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/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2986] [2987] [2988]
Underfull \hbox (badness 6876) in paragraph at lines 11681--11687
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
or two vari-ables, spec-i-fied via terms like
[2989]
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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
[2990] [2991]
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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
[2992] [2993]
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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)[]
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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/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[2994]
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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 11998--12000
\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
[2995] [2996] [2997]
Underfull \hbox (badness 10000) in paragraph at lines 12126--12127
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2998]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12207--12207
[]\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 12208--12208
[]\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[]
[2999] [3000] [3001]
Underfull \hbox (badness 10000) in paragraph at lines 12358--12359
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3002] [3003] [3004] [3005]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12597--12597
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3006]
Underfull \hbox (badness 10000) in paragraph at lines 12658--12660
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3007] [3008] [3009]
Underfull \hbox (badness 10000) in paragraph at lines 12817--12820
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 12817--12820
\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 12817--12820
\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"
[3010]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12901--12901
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3011]
Underfull \hbox (badness 10000) in paragraph at lines 12946--12952
[]\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 12946--12952
\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-
[3012] [3013] [3014]
Underfull \vbox (badness 10000) has occurred while \output is active [3015]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13160--13160
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
Underfull \vbox (badness 10000) has occurred while \output is active [3016]
Underfull \hbox (badness 10000) in paragraph at lines 13263--13271
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
[3017]
Underfull \hbox (badness 10000) in paragraph at lines 13289--13290
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3018] [3019] [3020] [3021]
Underfull \hbox (badness 3396) in paragraph at lines 13550--13553
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
num-ber of vari-ables, spec-i-fied via terms like
[3022]
Underfull \hbox (badness 10000) in paragraph at lines 13595--13597
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3023] [3024] [3025] [3026]
Underfull \hbox (badness 10000) in paragraph at lines 13819--13822
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 13819--13822
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 13852--13856
[][][]\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 13852--13856
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13852--13856
[][]\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 ,
[3027] [3028] [3029] [3030] [3031]
Underfull \hbox (badness 2158) in paragraph at lines 14142--14142
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3032] [3033]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14221--14221
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3034] [3035]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14355--14355
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3036] [3037]
Underfull \hbox (badness 4846) in paragraph at lines 14486--14489
[]\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
[3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048]
[3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15682--15682
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[3058] [3059] [3060]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 15892--15892
[]\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,
[3061]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15894--15894
[]\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 15896--15896
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
Underfull \hbox (badness 10000) in paragraph at lines 15915--15916
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 15915--15916
\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected
by \T1/pcr/m/n/10 ar.row
[3062] [3063] [3064]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16040--16040
[]\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 16041--16041
[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16053--16053
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[3065] [3066] [3067]) (./nlme-pkg.tex [3068]
Chapter 25.
[3069]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3070]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3071] [3072] [3073] [3074] [3075]
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,[]
[3076] [3077]
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 ---------------------------
---------------[]
[3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085]
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"),[]
[3086]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3087] [3088] [3089] [3090] [3091] [3092] [3093]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3094]
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
[3095] [3096] [3097] [3098] [3099]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3100]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[3101]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3102] [3103]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3104]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123]
[3124]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134] [3135]
[3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146]
[3147] [3148]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3149] [3150] [3151] [3152] [3153] [3154] [3155]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\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 ,
[3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\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
[3165]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\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 ,
[3166]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3167]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3168] [3169] [3170] [3171]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\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 ,
[3172]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3173]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3174]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3175] [3176] [3177]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3178]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3179] [3180] [3181]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3182] [3183] [3184]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7406--7414
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7429--7432
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3185] [3186] [3187]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\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
[3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3196] [3197] [3198] [3199] [3200]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3201]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.8572 \aliasA{sigma}{lmeObject}{sigma}
[3202] [3203] [3204] [3205] [3206]
[3207] [3208] [3209] [3210] [3211] [3212] [3213]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3214]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3215] [3216] [3217] [3218]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9686 ...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.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3219]
Underfull \hbox (badness 10000) in paragraph at lines 9706--9709
[]\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 9750--9753
[]\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 9750--9753
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3228] [3229] [3230]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3231]
Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3232] [3233] [3234]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3235] [3236]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3237]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10838--10840
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3238] [3239] [3240] [3241]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
[]\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 11131--11131
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
[3242] [3243] [3244] [3245] [3246] [3247]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11521--11521
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3248] [3249] [3250] [3251] [3252] [3253]
Underfull \hbox (badness 6268) in paragraph at lines 11908--11918
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3254] [3255] [3256] [3257]
Underfull \hbox (badness 10000) in paragraph at lines 12169--12175
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3258] [3259] [3260] [3261] [3262]
Underfull \hbox (badness 6876) in paragraph at lines 12491--12493
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
\T1/ptm/m/n/10 will be con-structed from
[3263] [3264]
Underfull \hbox (badness 2452) in paragraph at lines 12647--12654
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3265]
Underfull \hbox (badness 10000) in paragraph at lines 12712--12718
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13301--13301
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3275] [3276] [3277] [3278] [3279]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13666--13666
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3280]
Underfull \hbox (badness 10000) in paragraph at lines 13693--13696
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3281]
Underfull \hbox (badness 1838) in paragraph at lines 13736--13743
[]\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 13736--13743
\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 13793--13793
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3282]
Underfull \hbox (badness 10000) in paragraph at lines 13800--13803
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13800--13803
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13828--13831
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13828--13831
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3283]
Underfull \hbox (badness 10000) in paragraph at lines 13908--13911
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3284]
Underfull \hbox (badness 1472) in paragraph at lines 13933--13940
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3285]
Underfull \hbox (badness 10000) in paragraph at lines 14002--14004
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3286] [3287] [3288] [3289]
Underfull \hbox (badness 1215) in paragraph at lines 14282--14284
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3290] [3291] [3292] [3293]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14526--14526
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302]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.15179 ...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.15179 ...Extract Random Effects}{random.effects}
[3303] [3304] [3305]
[3306] [3307] [3308] [3309] [3310] [3311] [3312] [3313]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15827--15827
[]\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 15846--15846
[] \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 15847--15847
[] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),
tol = 7e-7)[]
[3314]
Underfull \hbox (badness 1009) in paragraph at lines 15877--15886
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3315] [3316]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16024--16024
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3317] [3318] [3319] [3320] [3321]
Underfull \hbox (badness 10000) in paragraph at lines 16359--16365
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3322]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16390--16390
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3323] [3324] [3325] [3326] [3327] [3328] [3329]
Underfull \hbox (badness 1728) in paragraph at lines 16879--16882
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3330] [3331] [3332] [3333] [3334]
Underfull \hbox (badness 1867) in paragraph at lines 17214--17223
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple 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 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3335]
Underfull \hbox (badness 1521) in paragraph at lines 17278--17286
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance
Underfull \hbox (badness 10000) in paragraph at lines 17278--17286
\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 1694) in paragraph at lines 17278--17286
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3336] [3337] [3338] [3339]
Underfull \hbox (badness 10000) in paragraph at lines 17525--17532
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3340] [3341] [3342] [3343] [3344] [3345] [3346]
Underfull \hbox (badness 10000) in paragraph at lines 18060--18070
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18060--18070
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3347]
Underfull \hbox (badness 3579) in paragraph at lines 18098--18103
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3348]
Underfull \hbox (badness 3579) in paragraph at lines 18162--18167
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3349]
Underfull \hbox (badness 3579) in paragraph at lines 18225--18230
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3350]
Underfull \hbox (badness 1577) in paragraph at lines 18286--18288
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18288--18293
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3351]
Underfull \hbox (badness 3579) in paragraph at lines 18351--18356
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18384--18393
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18384--18393
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3352]
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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/ptm/m
/n/10 , in which case a se-quence
[3353] [3354]
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\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3355] [3356]
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\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365]) (./nnet-pkg.tex
[3366]
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}
[3367]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3368] [3369] [3370]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3371]
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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)[]
[3372] [3373]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3374]) (./rpart-pkg.tex
Chapter 27.
[3375] [3376] [3377] [3378]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3379] [3380] [3381] [3382]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3383] [3384]
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[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3385] [3386]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3387]
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[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3388] [3389] [3390]
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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, ...)[]
[3391]
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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/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3392]
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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,[]
[3393] [3394] [3395] [3396] [3397] [3398]
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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 ',
[3399] [3400]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3401] [3402] [3403]) (./spatial-pkg.tex [3404]
Chapter 28.
[3405] [3406] [3407] [3408] [3409] [3410]
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[3411] [3412] [3413] [3414] [3415] [3416] [3417] [3418] [3419] [3420] [3421]
[3422] [3423]) (./survival-pkg.tex [3424]
Chapter 29.
[3425] [3426]
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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.[]
[3427] [3428]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again>
\relax
l.326 ... 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.326 ... Myelogenous Leukemia survival data}{aml}
[3429] [3430]
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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)[]
[3431]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3432] [3433]
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[]\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size,
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3435] [3436]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3437] [3438] [3439]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\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[]
[3440] [3441]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3442]
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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.1177 ...erapy for Stage B/C colon cancer}{colon}
[3443]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1270--1270
[] \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, ...)[]
[3444] [3445]
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[] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[]
[3446]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3447] [3448] [3449] [3450]
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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:: \T1/pt
m/m/n/10 onto ev-er-thing, in-clud-ing the spe-
Underfull \hbox (badness 10000) in paragraph at lines 1793--1808
\T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t
ime,status) ~ age +
[3451]
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[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.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 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3452]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3461] [3462] [3463]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3464] [3465] [3466] [3467]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3468]
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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
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3080--3080
[] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[]
[3469] [3470]
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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 )))[]
[3471] [3472]
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[] []
[3473] [3474] [3475]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3476] [3477] [3478] [3479] [3480]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3849--3849
[] \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 )))[]
[3481] [3482] [3483] [3484]
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[3486] [3487]
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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,[]
[3488] [3489] [3490]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3491]
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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[]
[3492]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3493]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3494] [3495]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3496] [3497]
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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, ...)[]
[3498] [3499] [3500]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3501]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5255--5255
[]\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)) +[]
[3502] [3503] [3504] [3505] [3506]
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[3508] [3509]
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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/ptm/m/n/10
, \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3510] [3511] [3512] [3513] [3514]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.6186 ...ata from a soldering experiment}{solder}
[3515] [3516]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3517] [3518] [3519] [3520] [3521]
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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,[]
[3522] [3523] [3524] [3525]
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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 ),[]
[3526] [3527] [3528]
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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 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3529]
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[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3530] [3531] [3532]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
form
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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample
test, the
[3533]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
[3534]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3535]
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3536]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3537] [3538] [3539]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
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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/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
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[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
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[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
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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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Chapter 1.
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
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[5]
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[]\T1/ptm/m/n/10 when [][]\T1/pcr/m/n/10 capabilities[][][]["long.double"] \T1/
ptm/m/n/10 is true, there are 10 such
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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-lar,
[8] [9] [10]
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[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
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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/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
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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 tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[32] [33] [34] [35]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2303--2303
[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
[36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2431--2433
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
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[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[38]
Underfull \hbox (badness 1107) in paragraph at lines 2502--2504
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[39] [40]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2669--2669
[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3337--3337
[]\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)[]
[51]
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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 3377--3377
[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3380--3380
[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
[52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3820--3822
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
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[] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive)
[62] [63] [64]
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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 or
[65] [66]
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
[67]
Underfull \hbox (badness 4595) in paragraph at lines 4468--4471
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
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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/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e
xclude = TRUE)[]
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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
[70] [71] [72]
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5097--5099
[]\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
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5509--5517
[]\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
[82] [83] [84] [85] [86] [87] [88] [89] [90]
Underfull \hbox (badness 1796) in paragraph at lines 6075--6083
[]\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 : / /
[91] [92]
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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_)))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6272--6272
[]\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}[]
[93] [94]
Underfull \hbox (badness 1242) in paragraph at lines 6411--6415
\T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel
ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment.
[95]
Underfull \hbox (badness 1635) in paragraph at lines 6474--6477
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
Underfull \hbox (badness 3009) in paragraph at lines 6478--6481
[]\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
[96]
Underfull \hbox (badness 1308) in paragraph at lines 6521--6529
[]\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
[97] [98]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6685--6685
[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
Underfull \vbox (badness 10000) has occurred while \output is active [99]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6735--6737
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 :
[100]
Underfull \hbox (badness 1997) in paragraph at lines 6862--6867
[]\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1
0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x
zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC
onnection\T1/ptm/m/n/10 ,
[101]
Underfull \hbox (badness 10000) in paragraph at lines 6900--6903
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 6900--6903
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[102] [103]
Underfull \hbox (badness 1406) in paragraph at lines 7082--7088
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
Underfull \hbox (badness 2173) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and
web-pages gen-er-ated by
Underfull \hbox (badness 2134) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 7102--7104
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[104]
Underfull \hbox (badness 1067) in paragraph at lines 7144--7151
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[105] [106]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 7346--7346
[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[108] [109]
Underfull \hbox (badness 1231) in paragraph at lines 7471--7477
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the
first el-e-
[110] [111] [112]
Underfull \hbox (badness 10000) in paragraph at lines 7683--7685
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[113] [114]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7828--7828
[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
[115] [116] [117] [118]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8066--8066
[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[119] [120]
Underfull \hbox (badness 10000) in paragraph at lines 8188--8198
[]\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 8188--8198
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
is a generic func-tion, meth-ods can be
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8220--8225
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[121] [122] [123] [124] [125] [126] [127]
Underfull \hbox (badness 1629) in paragraph at lines 8709--8721
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8709--8721
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
, and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[128] [129] [130] [131] [132] [133]
Underfull \hbox (badness 10000) in paragraph at lines 9157--9161
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[134]
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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})[]
[135]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9277--9277
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[136] [137]
Underfull \hbox (badness 5403) in paragraph at lines 9414--9416
[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9433--9435
[]\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
[138] [139] [140]
Underfull \hbox (badness 1603) in paragraph at lines 9658--9661
[]\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
[141] [142] [143] [144] [145] [146] [147] [148] [149]
Underfull \hbox (badness 1917) in paragraph at lines 10266--10271
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[150]
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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 10322--10322
[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[151] [152]
Underfull \hbox (badness 1168) in paragraph at lines 10424--10429
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
Underfull \hbox (badness 10000) in paragraph at lines 10463--10469
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
Underfull \hbox (badness 5403) in paragraph at lines 10470--10473
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[153] [154]
Underfull \hbox (badness 2828) in paragraph at lines 10629--10633
[][][]$\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 10629--10633
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
[155]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10662--10662
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[156]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10735--10735
[]\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, ..[]
[157] [158]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10882--10882
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[159] [160] [161]
Underfull \hbox (badness 6396) in paragraph at lines 11079--11087
[]\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 11088--11090
[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[162] [163] [164]
Underfull \hbox (badness 10000) in paragraph at lines 11305--11308
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[165] [166] [167] [168] [169] [170] [171] [172] [173]
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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
[174]
Underfull \hbox (badness 3039) in paragraph at lines 12017--12022
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
and
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[175] [176]
Underfull \hbox (badness 4569) in paragraph at lines 12199--12203
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 12199--12203
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[177] [178]
Underfull \hbox (badness 10000) in paragraph at lines 12314--12316
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13159--13159
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[190] [191] [192] [193] [194] [195]
Underfull \hbox (badness 2221) in paragraph at lines 13609--13618
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
Underfull \hbox (badness 1635) in paragraph at lines 13609--13618
\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[196] [197] [198] [199]
Underfull \hbox (badness 2253) in paragraph at lines 13870--13872
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[200] [201]
Underfull \hbox (badness 2573) in paragraph at lines 13987--13989
[]\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 =
[202] [203]
Underfull \hbox (badness 10000) in paragraph at lines 14142--14144
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[204] [205]
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
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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[]
[206]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[207]
Underfull \hbox (badness 10000) in paragraph at lines 14410--14413
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14420--14420
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[208]
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[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
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:[]
[209]
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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 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14556--14563
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14564--14568
[]\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,
[210] [211] [212]
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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)[]
[213] [214] [215]
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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[]
[216]
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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
[217]
Underfull \hbox (badness 6944) in paragraph at lines 15146--15149
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[218]
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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),[]
[219] [220]
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[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
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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)),[]
[221]
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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
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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
[222]
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[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls
Underfull \hbox (badness 4954) in paragraph at lines 15448--15450
\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
in this
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[]\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/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-rides
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
[223]
Underfull \hbox (badness 10000) in paragraph at lines 15482--15486
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
Underfull \hbox (badness 10000) in paragraph at lines 15482--15486
\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 15487--15495
[]\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
[224]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15595--15595
[]\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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Overfull \hbox (42.18039pt too wide) in paragraph at lines 15617--15617
[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
[226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16435--16435
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[238]
Underfull \hbox (badness 2418) in paragraph at lines 16544--16548
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
,
Underfull \hbox (badness 6510) in paragraph at lines 16551--16554
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
[239]
Underfull \hbox (badness 2326) in paragraph at lines 16586--16593
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[240] [241] [242]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16836--16836
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
[243]
Underfull \hbox (badness 1867) in paragraph at lines 16861--16868
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[244] [245] [246] [247]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17139--17139
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
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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 17219--17219
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
[249] [250] [251] [252]
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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)))
[253]
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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"))[]
[254] [255] [256]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17841--17841
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[257] [258] [259] [260]
Underfull \hbox (badness 2435) in paragraph at lines 18109--18111
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
[261]
Underfull \hbox (badness 2285) in paragraph at lines 18175--18177
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
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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.[]
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[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[262] [263]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
[264]
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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" :[]
[265] [266]
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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):[]
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 18702--18704
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[270] [271] [272] [273] [274] [275] [276] [277]
Underfull \hbox (badness 4699) in paragraph at lines 19275--19278
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[278] [279]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19403--19403
[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[280] [281]
Underfull \hbox (badness 4739) in paragraph at lines 19538--19540
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[282]
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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)[]
[283] [284] [285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1975) in paragraph at lines 20166--20169
[]\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
[291] [292] [293] [294] [295] [296]
Underfull \hbox (badness 1077) in paragraph at lines 20564--20569
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
[297]
Underfull \hbox (badness 10000) in paragraph at lines 20578--20585
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[298]
Underfull \hbox (badness 10000) in paragraph at lines 20652--20656
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[299] [300]
Underfull \hbox (badness 10000) in paragraph at lines 20801--20805
[]\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 20801--20805
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 20806--20813
[]\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-
[301] [302]
Underfull \hbox (badness 10000) in paragraph at lines 20937--20944
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[303]
Underfull \hbox (badness 10000) in paragraph at lines 21058--21062
[]\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
[304]
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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
Underfull \hbox (badness 6592) in paragraph at lines 21128--21133
\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 21128--21133
\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 21128--21133
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[305] [306] [307]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21295--21295
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21299--21299
[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[308]
Underfull \hbox (badness 3343) in paragraph at lines 21360--21364
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[309] [310]
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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,
pr = 0.2))),[]
[311] [312]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 21624--21624
[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
Underfull \hbox (badness 6380) in paragraph at lines 21669--21674
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
[313]
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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
[314]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21790--21790
[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
[315] [316]
Underfull \hbox (badness 1400) in paragraph at lines 21958--21962
[][][]\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 do
uble[][][] \T1/ptm/m/n/10 (class
[317] [318] [319]
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[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
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\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
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\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[320] [321] [322] [323] [324] [325] [326] [327] [328]
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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)[]
[329] [330]
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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'):
[331] [332] [333] [334]
Underfull \hbox (badness 2277) in paragraph at lines 23143--23146
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
\T1/ptm/m/n/10 are typ-i-cally prefer-able.
[335] [336]
Underfull \hbox (badness 10000) in paragraph at lines 23272--23275
[]\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc
r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.
0,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 1484) in paragraph at lines 23724--23732
[]\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 /
[343] [344]
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[345] [346] [347] [348] [349] [350] [351]
Underfull \hbox (badness 1448) in paragraph at lines 24310--24318
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[352] [353]
Underfull \hbox (badness 3849) in paragraph at lines 24425--24430
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[354]
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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-re-spond-
ing
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\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE))
\T1/ptm/m/n/10 which are also given by
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[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10
. If the en-vi-ron-ment is used as a hash
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[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
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\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[355] [356]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[357] [358] [359]
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[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[360] [361] [362]
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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-
[363] [364] [365] [366] [367]
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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-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
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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-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about 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 com-p
uted 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)
[368]
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
[369]
Underfull \hbox (badness 10000) in paragraph at lines 25488--25494
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
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\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
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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:[]
[370] [371] [372]
Underfull \hbox (badness 8189) in paragraph at lines 25747--25753
[]\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
[][][]
[373] [374] [375]
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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');
[376] [377] [378] [379]
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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
[380] [381]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 26346--26354
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[382] [383]
Underfull \hbox (badness 3271) in paragraph at lines 26565--26568
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[384] [385] [386]
Underfull \hbox (badness 3138) in paragraph at lines 26865--26871
[]\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 26865--26871
\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 26865--26871
\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 26878--26881
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
[387]
Underfull \hbox (badness 1389) in paragraph at lines 26904--26906
[]\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
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[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
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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
[388]
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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 26981--26987
\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 26981--26987
\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 26981--26987
\T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina
ry.universal" \T1/ptm/m/n/10 are no longer
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[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
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\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
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\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 26996--27003
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[389] [390] [391] [392]
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[]\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 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
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\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[394] [395]
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[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
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\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[396] [397] [398] [399]
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[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
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[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
\T1/ptm/m/n/10 which con-cate-nates and
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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[]
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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)[]
[400] [401] [402]
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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 =
[403] [404] [405] [406] [407] [408]
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[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m
/n/10 get[][][](name,envir =
[409]
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[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
see
[410] [411] [412]
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[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[413] [414] [415] [416] [417] [418] [419] [420] [421] [422]
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[] \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))[]
[423] [424]
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[426]
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[]\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"[]
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[]\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 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
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[428]
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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.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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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[]
[429]
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[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
[430]
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[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[431] [432]
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\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
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\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 /
[433] [434]
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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
[435] [436]
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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 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[437] [438]
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[]\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")[]
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[]\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")[]
[439]
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[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
[440] [441] [442] [443] [444]
Underfull \hbox (badness 4048) in paragraph at lines 30843--30848
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
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\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 ,
[445] [446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 2080) in paragraph at lines 31380--31390
[]\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.[]
[453] [454] [455] [456] [457] [458] [459]
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[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 31930--31932
[]\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
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[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 31939--31941
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 31942--31944
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[460] [461] [462] [463] [464] [465]
Underfull \hbox (badness 10000) in paragraph at lines 32347--32351
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[466] [467] [468] [469] [470]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32703--32703
[] \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"),[]
[471] [472] [473] [474] [475] [476] [477]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 33146--33146
[] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[]
[478] [479] [480] [481] [482] [483]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33581--33581
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[484] [485]
Underfull \hbox (badness 1158) in paragraph at lines 33685--33690
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal
and hex-adec-i-mal rep-re-sen-ta-tions
[486] [487]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 33870--33870
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[488] [489] [490]
Underfull \hbox (badness 8151) in paragraph at lines 34130--34133
[]\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 .
[491] [492] [493] [494]
Underfull \hbox (badness 10000) in paragraph at lines 34345--34350
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10
gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by =
[495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506]
[507] [508] [509]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 35333--35333
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[510] [511] [512]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 35585--35585
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 35587--35587
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[513]
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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[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 35630--35636
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[514] [515]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 35741--35741
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[516] [517] [518] [519]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36074--36074
[]\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)[]
[520]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[521] [522] [523] [524] [525] [526]
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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)[]
[527] [528] [529]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 36798--36798
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[530] [531]
Underfull \hbox (badness 6110) in paragraph at lines 36889--36899
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 36889--36899
\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
Underfull \hbox (badness 1237) in paragraph at lines 36889--36899
\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 36889--36899
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n 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 36889--36899
\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
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[]\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 36935--36941
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 36935--36941
\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 36947--36954
[]\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 36947--36954
\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 36947--36954
\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
[532] [533] [534] [535]
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[]\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/
m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
[536]
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
[537] [538] [539] [540] [541] [542] [543] [544]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 37821--37821
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[545] [546] [547]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[548]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[549] [550] [551] [552] [553] [554] [555]
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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, ....[]
[556]
Underfull \hbox (badness 10000) in paragraph at lines 38601--38608
[]\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 38601--38608
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38654--38654
[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[557] [558] [559] [560] [561]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 38965--38965
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[562] [563] [564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39130--39130
[]\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.
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[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
[565]
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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-
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\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.
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[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
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\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
[566]
Underfull \hbox (badness 2452) in paragraph at lines 39307--39310
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 39307--39310
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[567] [568] [569]
Underfull \hbox (badness 10000) in paragraph at lines 39495--39499
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
Underfull \hbox (badness 1584) in paragraph at lines 39510--39513
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[570] [571]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 39642--39642
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[572]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 39712--39712
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used
[573] [574] [575]
Underfull \hbox (badness 1082) in paragraph at lines 39856--39859
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577]
Underfull \hbox (badness 1038) in paragraph at lines 40047--40050
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[578] [579] [580] [581] [582] [583]
Underfull \hbox (badness 1442) in paragraph at lines 40408--40412
\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 =
[584] [585] [586]
Underfull \hbox (badness 4096) in paragraph at lines 40658--40661
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[587] [588]
Underfull \hbox (badness 7888) in paragraph at lines 40772--40776
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
length(bin) >
[589] [590]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40926--40926
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 40928--40928
[] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[]
[591]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40930--40930
[] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 40943--40945
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[592]
Underfull \hbox (badness 10000) in paragraph at lines 41023--41026
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[593] [594]
Underfull \hbox (badness 3872) in paragraph at lines 41141--41144
[]\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 .
[595]
Underfull \hbox (badness 5475) in paragraph at lines 41207--41211
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[596] [597] [598] [599] [600] [601]
Underfull \hbox (badness 10000) in paragraph at lines 41625--41632
\T1/ptm/m/n/10 is also 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 4467) in paragraph at lines 41681--41690
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 41681--41690
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
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[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 41691--41699
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
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\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[602]
Underfull \hbox (badness 1337) in paragraph at lines 41757--41765
\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
[603]
Underfull \hbox (badness 3460) in paragraph at lines 41820--41823
[][][]$\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-
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[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[604] [605] [606]
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[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[607] [608]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42176--42176
[]\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:[]
[609] [610]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 42279--42279
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 42281--42281
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
[611] [612] [613]
Underfull \hbox (badness 6542) in paragraph at lines 42555--42557
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
, and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[614] [615]
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
[616]
Underfull \hbox (badness 1708) in paragraph at lines 42742--42750
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 42742--42750
\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
[617]
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[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
and sup-press-ing the print-ing of er-ror mes-sages;
[618]
Underfull \hbox (badness 3895) in paragraph at lines 42834--42846
[]\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 42834--42846
\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 ,
[619] [620] [621] [622]
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[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[623] [624] [625] [626] [627] [628] [629]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 43623--43623
[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
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[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[]
[630]
Underfull \hbox (badness 2057) in paragraph at lines 43699--43705
[][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[
][][]\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 ,
Underfull \hbox (badness 3861) in paragraph at lines 43708--43713
[][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex
ists[][][]\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 ,
[631] [632]
Underfull \hbox (badness 1803) in paragraph at lines 43853--43856
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 3471) in paragraph at lines 43857--43864
[]\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
[633] [634] [635]
Underfull \hbox (badness 3668) in paragraph at lines 44072--44074
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[636] [637]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 44178--44178
[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44253--44253
[]\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 ...[]
[639] [640]
Underfull \hbox (badness 6220) in paragraph at lines 44391--44396
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 44391--44396
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
Underfull \hbox (badness 10000) in paragraph at lines 44412--44417
[]\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 4229) in paragraph at lines 44412--44417
\T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m
a-trix whose rows each
[641] [642]
Underfull \hbox (badness 2818) in paragraph at lines 44508--44514
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
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[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[643] [644]
Underfull \hbox (badness 1622) in paragraph at lines 44637--44639
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[645] [646] [647] [648] [649]
Underfull \hbox (badness 2846) in paragraph at lines 45000--45004
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[650]
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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-dard
' reg-exps, in-clud-ing el-e-ments named
[651]) (./compiler-pkg.tex [652]
Chapter 2.
[653]
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 be us
ed to con-trol com-piler op-er-a-tion. There are cur-
Underfull \hbox (badness 10000) in paragraph at lines 106--120
\T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[654] [655] [656]) (./datasets-pkg.tex
Chapter 3.
[657] [658] [659] [660] [661]
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,[]
[662]
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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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[664] [665] [666] [667]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 702--705
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[668] [669]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 835--838
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[670] [671]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\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.
[672] [673]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1146--1149
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[674] [675] [676] [677] [678]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456
[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[679] [680]
Underfull \hbox (badness 10000) in paragraph at lines 1541--1544
[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1541--1544
\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[681] [682] [683]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1730--1733
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[684]
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[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
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[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[685] [686]
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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 1949--1949
[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[687] [688] [689] [690]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2152--2155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[691] [692] [693]
Overfull \vbox (4.29591pt too high) has occurred while \output is active
[694] [695] [696] [697] [698]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[699]
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[700]
Underfull \vbox (badness 2376) has occurred while \output is active [701]
[702]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[703] [704]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[705]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3146--3146
[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[706] [707] [708] [709] [710] [711] [712]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[713] [714]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[715]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[716]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[717]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
Underfull \hbox (badness 10000) in paragraph at lines 3998--4000
[]\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 3998--4000
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729]
[730] [731]) (./grDevices-pkg.tex [732]
Chapter 4.
[733] [734] [735] [736]
Underfull \hbox (badness 1365) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
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[]\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/ptm/m/n/1
0 in
[737] [738]
Underfull \hbox (badness 10000) in paragraph at lines 379--387
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[739] [740]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 516--516
[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
Underfull \hbox (badness 5175) in paragraph at lines 1186--1188
[]\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
[751] [752] [753]
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
Underfull \hbox (badness 1173) in paragraph at lines 1399--1402
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[754] [755] [756] [757] [758] [759] [760] [761]
Underfull \hbox (badness 1565) in paragraph at lines 1887--1892
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1887--1892
\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
[762]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
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[]\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-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[763] [764]
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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
[765] [766]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[767] [768]
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\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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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
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[769] [770]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
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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)
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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)[]
[772] [773] [774] [775] [776]
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[778] [779] [780] [781]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3243--3243
[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[782]
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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 3328--3328
[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[783] [784]
Underfull \hbox (badness 10000) in paragraph at lines 3484--3489
[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[785] [786]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3558--3558
[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[]
[787]
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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)[]
[788]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
[789]
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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 ,
[790]
Underfull \hbox (badness 2189) in paragraph at lines 3815--3820
[]\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we
ll for shad-ing points or lines in up to five groups,
Underfull \hbox (badness 10000) in paragraph at lines 3853--3857
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[791]
Underfull \vbox (badness 10000) has occurred while \output is active [792]
Underfull \hbox (badness 5260) in paragraph at lines 3983--3986
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[793] [794] [795] [796] [797]
Underfull \hbox (badness 5939) in paragraph at lines 4315--4320
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[798] [799] [800] [801] [802] [803]
Underfull \hbox (badness 10000) in paragraph at lines 4719--4724
[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
/ devnet / actionscript /
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\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[804] [805]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4834--4834
[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[806] [807]
Underfull \hbox (badness 1348) in paragraph at lines 5039--5042
[]\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
[808]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5063--5063
[]\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 5104--5110
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[809]
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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"
[810]
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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
[811] [812] [813]
Underfull \hbox (badness 7344) in paragraph at lines 5459--5461
[]\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 5470--5474
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[814] [815]
Underfull \hbox (badness 1552) in paragraph at lines 5596--5605
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[816]
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[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[817] [818]
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[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[819]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
[820] [821]
Underfull \hbox (badness 10000) in paragraph at lines 5963--5965
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
for on-screen de-vices and to
[822] [823] [824] [825] [826]
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[]\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 6344--6347
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[827] [828] [829] [830] [831] [832]
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[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
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[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
[833] [834] [835] [836]
Underfull \hbox (badness 10000) in paragraph at lines 6949--6954
[]\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 y
pos\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 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[837]
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[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
[838]
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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 :
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7105--7105
[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
[839]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[840]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
[841]
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[842]
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[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[843]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[844] [845]
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\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 7613--7616
[]\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 /
[846] [847]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[848] [849] [850]) (./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 =
[851] [852] [853]
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[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[854] [855] [856] [857]
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[] \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
[858] [859]
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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[]
[860]
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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
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[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[861] [862]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781
[] \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 818--818
[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
[863] [864] [865]
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[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/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-able.
Overfull \hbox (106.98032pt too wide) in paragraph at lines 981--981
[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[]
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[]\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 985--985
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
[866] [867] [868] [869]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1269--1269
[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
[870] [871] [872]
Underfull \hbox (badness 1024) in paragraph at lines 1431--1439
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[873] [874]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1535--1535
[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
= "grey40",[]
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[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[875] [876] [877] [878] [879]
Underfull \hbox (badness 10000) in paragraph at lines 1846--1852
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10
contourplot[][][] \T1/ptm/m/n/10 (and
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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 = "")[]
[880] [881]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[882] [883]
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[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, 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))[]
[884] [885]
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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 = "",[]
[886]
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[]\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
[887]
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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
[888]
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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[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
[889]
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[]\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[]
[890] [891] [892]
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[893]
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[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[894] [895]
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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
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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 :[]
[896]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[897] [898] [899]
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[]\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, ...)[]
[900] [901]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
raster im-ages are used when the
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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/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[902] [903] [904]
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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"),[]
[905]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[906] [907]
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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])[]
[908]
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[] \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 [909]
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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))[]
[910]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[911] [912]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4044--4044
[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[913] [914]
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[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
[915]
Underfull \hbox (badness 3930) in paragraph at lines 4277--4279
[]\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
[916] [917] [918] [919] [920]
Underfull \hbox (badness 1286) in paragraph at lines 4588--4591
\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
[921] [922]
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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))[]
[923]
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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/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[924] [925]
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[926] [927]
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[928 </usr/src/RPM/BUILD/R-4.0.2/library/graphics/help/figures/mai.pdf>]
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[929 </usr/src/RPM/BUILD/R-4.0.2/library/graphics/help/figures/oma.pdf>]
[930]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[931]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5464--5464
[]\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,[]
Underfull \vbox (badness 10000) has occurred while \output is active [932]
[933] [934] [935] [936] [937]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5830--5830
[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5831--5831
[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
[938]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again>
\relax
l.5890 \aliasA{plot}{plot.default}{plot}
[939] [940] [941] [942] [943]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6222--6222
[]\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[]
[944] [945] [946] [947] [948] [949]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[950] [951]
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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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[][]
[952 </usr/src/RPM/BUILD/R-4.0.2/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,[]
[953]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6920--6920
[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[955]
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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)))))[]
[956]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[957] [958] [959] [960]
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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))[]
[961] [962] [963] [964] [965] [966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7754--7754
[]\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):[]
[967]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[968] [969] [970] [971] [972]
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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,[]
[973] [974] [975]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8297--8297
[]\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, ...)[]
[976] [977]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
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[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[978]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[979]
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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),[]
[980] [981]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[982] [983]
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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...")[]
[984]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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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 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[985]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8968 \HeaderA{units}{Graphical Units}{units}
[986]
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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
[987] [988]
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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)[]
[989]) (./grid-pkg.tex [990]
Chapter 6.
[991] [992] [993] [994] [995] [996] [997] [998]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117
[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1009] [1010] [1011] [1012]
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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
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[1019] [1020] [1021]
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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")[]
[1022]
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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 ,
[1023]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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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
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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
[1027] [1028] [1029]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1030]
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
[1031] [1032]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[1033] [1034] [1035] [1036]
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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"))))[]
[1042]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
"bottom")))[]
[1043]
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1044] [1045]
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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,[]
[1046] [1047] [1048]
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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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[1061]
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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
[1062]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1063] [1064] [1065]
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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 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
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[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
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\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1086] [1087] [1088] [1089] [1090]
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
[1091]
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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
[1092]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1093] [1094]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
do-ing some-thing like \T1/pcr/m/n/10 depth
[1095]
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[1097] [1098]
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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"))))[]
[1099]) (./methods-pkg.tex [1100]
Chapter 7.
[1101] [1102]
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\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1103] [1104] [1105]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1106] [1107]
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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[]
[1108]
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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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[1122] [1123] [1124]
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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[]
[1125] [1126]
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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 c
an be an ob-ject of class
[1127] [1128] [1129]
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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 =
[1130] [1131]
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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
[1132] [1133] [1134]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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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
[1135]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1136] [1137] [1138]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
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[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
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\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1146] [1147]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1148]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these
classes takes spe-cial ar-gu-ments
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[]
[1149] [1150]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
=
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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1151]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
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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
[1152] [1153] [1154]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1155] [1156] [1157]
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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,[]
[1158]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1159] [1160] [1161]
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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 ,
[1162] [1163] [1164]
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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
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1169]
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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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[1171]
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[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1172] [1173]
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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
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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/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
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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
[1185]
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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
[1186] [1187]
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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
[1188]
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[1190] [1191]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6973 \aliasA{S4}{S3Part}{S4}
[1192]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
[1193] [1194]
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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")[]
[1195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again>
\relax
l.7229 \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.7231 \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.7232 \aliasA{Math}{S4groupGeneric}{Math}
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th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7235 \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
[1196]
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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/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
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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 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
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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 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1197] [1198]
Underfull \hbox (badness 1694) in paragraph at lines 7472--7474
[]\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 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1199] [1200]
Underfull \hbox (badness 1019) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
\T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1212]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622
[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1213]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697
[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1214] [1215] [1216] [1217]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959
[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1218] [1219] [1220]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167
[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1221] [1222] [1223]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429
[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
[1224] [1225] [1226] [1227]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737
[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1228]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847
[]\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 9858--9858
[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238]
Underfull \hbox (badness 10000) in paragraph at lines 10556--10558
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\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 10564--10568
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1239] [1240] [1241]) (./parallel-pkg.tex [1242]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1243]
Underfull \hbox (badness 4242) in paragraph at lines 96--98
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1244] [1245]
Underfull \hbox (badness 1024) in paragraph at lines 213--216
[]\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
[1246] [1247] [1248]
Underfull \hbox (badness 10000) in paragraph at lines 449--451
[]\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
[1249] [1250] [1251] [1252] [1253]
Underfull \hbox (badness 1917) in paragraph at lines 755--764
[]\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 755--764
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1254]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 848--848
[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1255] [1256] [1257]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1039--1039
[]\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 1043--1043
[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1258] [1259]
Underfull \hbox (badness 5388) in paragraph at lines 1158--1163
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 1182--1190
[]\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
[1260]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1219--1219
[]\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)[]
[1261]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1335--1335
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
[1262]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1349--1349
[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
Underfull \hbox (badness 1577) in paragraph at lines 1378--1381
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1263]
Underfull \hbox (badness 3375) in paragraph at lines 1425--1427
[]\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
[1264] [1265]) (./splines-pkg.tex [1266]
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
[1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1275]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
-1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1276] [1277]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1278] [1279] [1280]) (./stats-pkg.tex
Chapter 10.
[1281]
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 o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
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[]
[1282] [1283] [1284] [1285] [1286]
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[]
[1287]
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)
[1288] [1289] [1290] [1291] [1292] [1293]
Underfull \hbox (badness 1024) in paragraph at lines 879--881
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303]
Underfull \hbox (badness 10000) in paragraph at lines 1541--1545
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1541--1545
\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1541--1545
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1304]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1617--1617
[] \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 1620--1620
[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
[1305] [1306]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767
[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
[1307]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1779--1779
[]\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 :[
]
[1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318]
[1319] [1320]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2770--2770
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1321] [1322] [1323] [1324]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3010--3010
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1325] [1326] [1327]
Underfull \hbox (badness 10000) in paragraph at lines 3220--3222
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1328]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3269--3269
[]\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 3270--3270
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1329] [1330] [1331] [1332] [1333] [1334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3661--3661
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1335] [1336] [1337] [1338]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3940--3940
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1339] [1340] [1341] [1342] [1343]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4229--4229
[]\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 4230--4230
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1344] [1345] [1346]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4469--4469
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1347] [1348] [1349]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4644--4644
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1350]
Underfull \hbox (badness 3989) in paragraph at lines 4738--4745
[]\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 =
[1351] [1352] [1353] [1354] [1355] [1356]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5123--5123
[]\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 5125--5125
[]\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))[]
[1357] [1358] [1359]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5346--5346
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5364--5364
[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
Underfull \hbox (badness 2680) in paragraph at lines 5391--5393
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is
given by
[1360] [1361] [1362]
Underfull \hbox (badness 1436) in paragraph at lines 5574--5579
[]\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 5574--5579
\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 5574--5579
\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 ,
[1363] [1364] [1365]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5777--5777
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1366] [1367] [1368]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5944--5944
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1369] [1370] [1371]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6129--6129
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1372]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6237--6237
[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
[1373]
Underfull \hbox (badness 10000) in paragraph at lines 6304--6309
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1374] [1375] [1376] [1377]
Underfull \hbox (badness 5954) in paragraph at lines 6500--6502
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1378]
Underfull \hbox (badness 2503) in paragraph at lines 6582--6585
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6586--6588
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6589--6594
\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,
Underfull \hbox (badness 7238) in paragraph at lines 6625--6628
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1379]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6660--6660
[]\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 6675--6675
[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6690--6690
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
Underfull \vbox (badness 10000) has occurred while \output is active [1380]
[1381] [1382] [1383]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6934--6934
[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
[1384] [1385] [1386] [1387] [1388] [1389]
Underfull \hbox (badness 10000) in paragraph at lines 7333--7337
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1390]
Underfull \hbox (badness 6493) in paragraph at lines 7432--7435
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1391] [1392]
Underfull \hbox (badness 10000) in paragraph at lines 7569--7572
[]\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 =
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Underfull \hbox (badness 10000) in paragraph at lines 7981--7986
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
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Underfull \hbox (badness 1210) in paragraph at lines 8336--8338
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
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[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
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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))[]
[1413] [1414]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8985--8985
[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
[1415] [1416] [1417] [1418] [1419] [1420]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9412--9412
[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
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[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
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Underfull \hbox (badness 7291) in paragraph at lines 9592--9594
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of
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Underfull \hbox (badness 6944) in paragraph at lines 10070--10076
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1430] [1431] [1432] [1433]
Underfull \hbox (badness 3758) in paragraph at lines 10284--10287
[]\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
[1434] [1435] [1436]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10528--10528
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
Underfull \hbox (badness 4518) in paragraph at lines 10554--10559
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1437]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1438]
Underfull \hbox (badness 1112) in paragraph at lines 10647--10653
[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
Underfull \hbox (badness 10000) in paragraph at lines 10698--10701
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
fitted.values \T1/ptm/m/n/10 and
[1439] [1440] [1441]
Underfull \hbox (badness 2142) in paragraph at lines 10915--10918
[]\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 ^^@
[1442] [1443]
Underfull \hbox (badness 1708) in paragraph at lines 10996--11000
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
Underfull \hbox (badness 10000) in paragraph at lines 11038--11044
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
[1444]
Underfull \hbox (badness 1418) in paragraph at lines 11076--11081
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1445] [1446]
Underfull \hbox (badness 2635) in paragraph at lines 11209--11212
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1447] [1448]
Underfull \hbox (badness 1694) in paragraph at lines 11392--11395
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1449] [1450]
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
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[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
[1451]
Underfull \hbox (badness 10000) in paragraph at lines 11539--11543
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1452] [1453] [1454] [1455] [1456]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11861--11861
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11876 \aliasA{hat}{influence.measures}{hat}
[1457]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11936--11936
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
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[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
[1458]
Underfull \hbox (badness 1062) in paragraph at lines 12001--12006
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12018--12020
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1459] [1460] [1461] [1462]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12272--12272
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
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[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
[1463]
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[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1464] [1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 12616--12618
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
[1468]
Underfull \hbox (badness 4739) in paragraph at lines 12639--12641
[]\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
[1469]
Underfull \hbox (badness 2753) in paragraph at lines 12708--12710
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1470] [1471] [1472]
Underfull \hbox (badness 6910) in paragraph at lines 12946--12948
[]\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
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[]\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 12952--12956
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 13659--13659
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1484]
Underfull \hbox (badness 4518) in paragraph at lines 13703--13708
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486]
Underfull \hbox (badness 10000) in paragraph at lines 13902--13906
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
,
[1487] [1488] [1489] [1490] [1491]
Underfull \hbox (badness 1163) in paragraph at lines 14236--14244
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1492] [1493]
Underfull \hbox (badness 4518) in paragraph at lines 14356--14361
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1494] [1495] [1496]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14544--14544
[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1497] [1498] [1499] [1500] [1501]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14888--14888
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1502] [1503]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14982--14982
[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1504] [1505] [1506] [1507] [1508] [1509]
Underfull \hbox (badness 2726) in paragraph at lines 15388--15391
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1510]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15482--15482
[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 16108--16108
[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1521] [1522]
Underfull \hbox (badness 1490) in paragraph at lines 16246--16251
\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
[1523]
Underfull \hbox (badness 1648) in paragraph at lines 16312--16314
[]\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 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
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\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1524]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16397--16397
[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= contr.poly))[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 16955--16955
[]\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[]
[1534] [1535] [1536]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17187--17187
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 17948--17948
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1549] [1550] [1551]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18111--18111
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18158--18158
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1552]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18205--18205
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560]
Underfull \hbox (badness 1248) in paragraph at lines 18703--18706
[]\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
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[]\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
[1561]
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\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
Underfull \hbox (badness 2042) in paragraph at lines 18782--18784
[]\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
[1562] [1563]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18888--18888
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
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[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
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[]\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 18972--18972
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18975--18975
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
[1565]
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19010--19021
\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
[1566]
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1567] [1568] [1569]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19299--19299
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1570] [1571]
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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
[1572] [1573] [1574] [1575] [1576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19729--19729
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1577] [1578]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19817--19817
[] \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 19819--19819
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19821--19821
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1579]
Underfull \hbox (badness 10000) in paragraph at lines 19867--19873
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 3049) in paragraph at lines 19908--19912
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1580] [1581] [1582] [1583]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20161--20161
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 1194) in paragraph at lines 20171--20174
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1584]
Underfull \hbox (badness 1107) in paragraph at lines 20229--20231
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1585]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20284--20284
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20291--20291
[]\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)[]
[1587]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20385--20385
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1588] [1589]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20514--20514
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1590]
Underfull \hbox (badness 7740) in paragraph at lines 20577--20579
[]\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
[1591]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20625--20625
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1592]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20717--20717
[] \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 20722--20722
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603]
[1604] [1605]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21577--21577
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
equal typically[]
[1606]
Underfull \hbox (badness 6859) in paragraph at lines 21644--21651
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21655--21661
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617]
[1618]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22401--22401
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1619] [1620] [1621] [1622] [1623]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22685--22685
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22686--22686
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1624] [1625] [1626] [1627] [1628]
Underfull \hbox (badness 1337) in paragraph at lines 23012--23018
[]\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
[1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23579--23579
[] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[]
[1637] [1638]
Underfull \hbox (badness 1028) in paragraph at lines 23720--23723
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1639] [1640]
Underfull \hbox (badness 10000) in paragraph at lines 23830--23833
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1641]
Underfull \hbox (badness 7944) in paragraph at lines 23885--23887
[]\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,levels =
[1642]
Underfull \hbox (badness 7944) in paragraph at lines 23947--23949
[]\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,levels =
[1643] [1644]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24049--24049
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1645] [1646] [1647]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24269--24269
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1648]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24373--24373
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
[1649]
Underfull \hbox (badness 1033) in paragraph at lines 24416--24422
\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 24437--24440
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1650]
Underfull \hbox (badness 2134) in paragraph at lines 24506--24510
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24519--24519
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1651]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24548--24548
[]\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 24560--24560
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
[1652] [1653] [1654] [1655] [1656] [1657] [1658]
Underfull \hbox (badness 6268) in paragraph at lines 25015--25020
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/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 ,
[1659]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 25043--25043
[] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[]
[1660] [1661] [1662]
Underfull \hbox (badness 1867) in paragraph at lines 25220--25222
[]\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 25235--25239
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback =
use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25235--25239
\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 25271--25271
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
[1663] [1664] [1665]
Underfull \hbox (badness 2495) in paragraph at lines 25461--25470
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1666]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25543--25543
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
[1667]
Underfull \hbox (badness 1412) in paragraph at lines 25550--25552
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1668]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25637--25637
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25662--25662
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25665--25665
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1669] [1670] [1671]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 25889--25889
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 25893--25899
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1672]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25939--25939
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25960--25960
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1673]
Underfull \hbox (badness 1019) in paragraph at lines 26022--26027
\T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow
\T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value
[1674] [1675]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26152--26152
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1676] [1677] [1678] [1679] [1680] [1681]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26531--26531
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1682] [1683]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26712--26712
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
[1684]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26718--26718
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean) f
or when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26727--26727
[]\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 26728--26728
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
[1685]
Underfull \hbox (badness 2922) in paragraph at lines 26797--26802
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26834--26834
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
[1686]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26837--26837
[] \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 26846--26846
[] \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 26847--26847
[] \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 26851--26851
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1687]
Underfull \hbox (badness 3240) in paragraph at lines 26905--26908
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26926--26926
[] \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 26929--26929
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1688]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27012--27012
[] \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 27016--27016
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
[1689]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 27026--27026
[] \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 27031--27031
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
Underfull \hbox (badness 2922) in paragraph at lines 27067--27073
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1690]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27089--27089
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27105--27105
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1691] [1692]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 27219--27219
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1693]
Underfull \hbox (badness 2922) in paragraph at lines 27281--27286
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27319--27319
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1694]
Underfull \hbox (badness 2922) in paragraph at lines 27368--27373
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1695]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27399--27399
[]\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 27433--27438
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1696]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27458--27458
[]\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 27462--27462
[]\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 27482--27482
[] \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 27492--27492
[] \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[]
[1697]
Underfull \hbox (badness 2922) in paragraph at lines 27527--27532
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27549--27549
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1698]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27567--27567
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
Underfull \hbox (badness 6493) in paragraph at lines 27619--27624
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1699]
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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
[1714] [1715] [1716]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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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
[1719]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1720]
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1721] [1722]
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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)
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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
[1725] [1726] [1727] [1728]
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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",[]
[1729]
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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
[1730]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1731]
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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 giv
en 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)[]
[1748] [1749]
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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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[1751] [1752]
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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-
e-sis, must be one of
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[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i
-tive nu-meric tol-er-ance, used in
[1762] [1763] [1764]
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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)[]
[1765] [1766]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
= getOption("ts.eps"), ...)[]
[1767]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
[1768]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1769]
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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 "")[]
[1770]) (./stats4-pkg.tex
Chapter 11.
[1771] [1772] [1773]
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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[]
[1775] [1776] [1777] [1778]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}
[1779] [1780] [1781])
(./tcltk-pkg.tex [1782]
Chapter 12.
[1783] [1784] [1785] [1786]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
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-ing
any Tk or Tcl com-mand by sim-ply run-ning
[1791] [1792] [1793] [1794] [1795] [1796]
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[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
[1797] [1798] [1799] [1800] [1801]
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1802]) (./tools-pkg.tex
Chapter 13.
[1803]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1804]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
which will be eval-u-ated via
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1805]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1806]
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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/1
0 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/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1807]
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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-gine
to use. Over-rides any
[1808] [1809]
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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, ...)[]
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
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\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
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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/p
tm/m/n/10 and
[1821]
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[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
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[] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[]
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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","Enhances")\T1/ptm/
m/n/10 .
[1829] [1830] [1831]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
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[1832] [1833] [1834]
[1835]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
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[]\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[]
[1836]
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[] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[]
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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
[1837]
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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
[1838]
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[]\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[]
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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","Enhances")\T1/ptm/
m/n/10 .
[1839]
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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/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[]
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[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
= TRUE)[]
[1840] [1841] [1842] [1843]
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[]
[1844]
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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
[1845] [1846] [1847] [1848] [1849]
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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-to
r 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"))[]
[1855] [1856] [1857] [1858]
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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
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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 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1863]
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[] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[]
[1864]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
sys-tem, as from
[1865] [1866] [1867]
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[] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[]
[1868] [1869]
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[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright,
bugs)
Underfull \hbox (badness 10000) in paragraph at lines 4448--4451
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
[1870]
Underfull \hbox (badness 6859) in paragraph at lines 4464--4469
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 4472--4478
[]\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 4472--4478
\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
[1871] [1872] [1873] [1874]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4730--4730
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4731--4731
[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[]
Underfull \hbox (badness 3240) in paragraph at lines 4743--4746
[]\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 4747--4757
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4782--4788
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4782--4788
\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 ',
[1875]
Underfull \hbox (badness 1571) in paragraph at lines 4810--4814
[]\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 4836--4841
\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
[1876] [1877] [1878]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1879] [1880] [1881] [1882]
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[]
[1883]
Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383
\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1884]
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
[1885]
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"))[]
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[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1886] [1887]
Underfull \hbox (badness 1946) in paragraph at lines 626--630
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1888]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 676--676
[]\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 683--683
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 684--684
[]\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 685--685
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Underfull \hbox (badness 10000) in paragraph at lines 719--725
[]\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 719--725
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1889] [1890]
Underfull \hbox (badness 4505) in paragraph at lines 855--861
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1891] [1892] [1893]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1029--1029
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1894]
Underfull \hbox (badness 1748) in paragraph at lines 1094--1102
[]\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 1094--1102
\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 1661) in paragraph at lines 1094--1102
\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 1094--1102
\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 1106--1108
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1895]
Underfull \hbox (badness 10000) in paragraph at lines 1214--1217
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1896]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1297--1297
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1799--1799
[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1834--1834
[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1905] [1906]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1980--1980
[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1907] [1908]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2132--2132
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1909]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2184--2184
[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1910] [1911] [1912]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2353--2353
[] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2376--2376
[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[1913] [1914]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2496--2496
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1915]
Underfull \hbox (badness 1082) in paragraph at lines 2570--2574
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2575 ... the Clipboard in MS Windows}{clipboard}
Underfull \hbox (badness 1163) in paragraph at lines 2606--2608
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1916] [1917]
Underfull \hbox (badness 10000) in paragraph at lines 2694--2696
[]\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
[1918] [1919] [1920]
Underfull \hbox (badness 10000) in paragraph at lines 2911--2913
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1921] [1922] [1923] [1924]
Underfull \hbox (badness 1762) in paragraph at lines 3205--3208
[]\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 =
[1925]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3298--3298
[]\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 '[]
[1926]
Underfull \hbox (badness 2452) in paragraph at lines 3374--3377
[]\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
[1927] [1928] [1929] [1930] [1931] [1932]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3783--3783
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[1933] [1934]
Underfull \hbox (badness 10000) in paragraph at lines 3867--3871
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is
op-tional on Win-dows: use
Underfull \hbox (badness 1072) in paragraph at lines 3924--3932
[]\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
[1935]
Underfull \hbox (badness 1231) in paragraph at lines 4001--4013
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 4015--4020
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method =
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 4015--4020
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
of
Underfull \hbox (badness 1331) in paragraph at lines 4015--4020
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
brack-ets are op-tional. See
[1936] [1937]
Underfull \hbox (badness 4660) in paragraph at lines 4135--4138
\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
Underfull \hbox (badness 10000) in paragraph at lines 4159--4161
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1938] [1939] [1940]
Underfull \hbox (badness 1565) in paragraph at lines 4344--4348
[]\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
[1941]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4427--4427
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[1942]
Underfull \hbox (badness 1931) in paragraph at lines 4462--4469
[]\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)
[1943] [1944] [1945] [1946] [1947]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4786--4786
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.4857 ...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.4857 ...mat Unordered and Ordered Lists}{format}
[1949] [1950] [1951]
[1952] [1953] [1954] [1955] [1956]
Underfull \hbox (badness 1622) in paragraph at lines 5376--5380
[]\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
[1957] [1958] [1959] [1960] [1961]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 5698--5698
[]\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 5710--5710
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
[1962] [1963]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5843--5843
[] \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 5844--5844
[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
[1964] [1965] [1966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6054--6054
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1967]
Underfull \hbox (badness 10000) in paragraph at lines 6138--6140
[]\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
[1968]
Underfull \hbox (badness 1502) in paragraph at lines 6187--6192
[]\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 6187--6192
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1969] [1970]
Underfull \hbox (badness 10000) in paragraph at lines 6360--6369
[]\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 6360--6369
\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
[1971]
Underfull \hbox (badness 2150) in paragraph at lines 6424--6427
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6440--6443
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search
database for sub-se-quent use by
[1972] [1973]
Underfull \hbox (badness 3118) in paragraph at lines 6562--6564
[]\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
[1974] [1975]
Underfull \hbox (badness 5091) in paragraph at lines 6736--6738
[]\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
[1976]
Underfull \hbox (badness 5331) in paragraph at lines 6752--6758
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6752--6758
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6752--6758
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6766--6773
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
Underfull \hbox (badness 1270) in paragraph at lines 6781--6791
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
[1977]
Underfull \hbox (badness 10000) in paragraph at lines 6824--6827
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be
Underfull \hbox (badness 10000) in paragraph at lines 6824--6827
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
Underfull \hbox (badness 1424) in paragraph at lines 6832--6835
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 6889--6893
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
[1978]
Underfull \hbox (badness 2376) in paragraph at lines 6903--6910
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 6903--6910
\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 6903--6910
\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 6911--6914
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1979]
Underfull \hbox (badness 1314) in paragraph at lines 6990--6997
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
Underfull \hbox (badness 10000) in paragraph at lines 7047--7052
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7070--7070
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
[1980]
Underfull \hbox (badness 5133) in paragraph at lines 7106--7110
[]\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 7120--7123
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1981]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7167--7167
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1982] [1983]
Underfull \hbox (badness 4132) in paragraph at lines 7287--7289
[]\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
[1984] [1985] [1986]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7454--7454
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1987] [1988]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7597--7597
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1989]
Underfull \hbox (badness 10000) in paragraph at lines 7637--7639
[]\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
[1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 7825--7827
[]\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 7830--7832
[]\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
[1992] [1993] [1994] [1995]
Underfull \hbox (badness 1859) in paragraph at lines 8058--8061
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1996]
Underfull \hbox (badness 1655) in paragraph at lines 8152--8155
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8163--8163
[]\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 8171--8171
[]\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):[]
[1997]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8179--8179
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1998]
Underfull \hbox (badness 1917) in paragraph at lines 8266--8268
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[1999] [2000] [2001] [2002]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8538--8538
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8539--8539
[] \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 8540--8540
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[2003]
Underfull \hbox (badness 10000) in paragraph at lines 8568--8570
[]\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 8582--8584
[]\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 8590--8595
[]\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,
[2004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8636--8636
[] \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 8637--8637
[] \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[]
[2005] [2006]
Underfull \hbox (badness 10000) in paragraph at lines 8766--8771
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8766--8771
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8766--8771
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8773--8776
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[2007]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8889--8889
[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8890--8890
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[2008] [2009] [2010]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9061--9061
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[2011]
Underfull \hbox (badness 1789) in paragraph at lines 9192--9194
[]\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
[2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020]
Underfull \hbox (badness 5203) in paragraph at lines 9765--9768
[]\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
[2021] [2022]
Underfull \hbox (badness 1394) in paragraph at lines 9991--9998
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
, try-ing to com-plete
[2023]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10015--10015
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[2024] [2025]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10176--10176
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[2026] [2027] [2028]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10357--10357
[]\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[]
[2029]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10443--10443
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10446--10446
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10451--10451
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2030]
Underfull \hbox (badness 2027) in paragraph at lines 10523--10526
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[2031] [2032] [2033] [2034]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10795--10795
[]\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 10796--10796
[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
Underfull \hbox (badness 10000) in paragraph at lines 10803--10808
[]\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 10803--10808
\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 10803--10808
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2035] [2036] [2037]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11036--11036
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2038] [2039] [2040] [2041] [2042]
Underfull \hbox (badness 10000) in paragraph at lines 11297--11301
\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 11315--11315
[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11320--11320
[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[2043] [2044]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11453--11453
[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 11454--11454
[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
[2045] [2046]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11589--11589
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[2047]
Underfull \hbox (badness 1917) in paragraph at lines 11713--11716
[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
Underfull \hbox (badness 4328) in paragraph at lines 11713--11716
\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
[2048]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 11736--11736
[]\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 '[]
[2049]
Underfull \hbox (badness 10000) in paragraph at lines 11799--11801
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
[2050]
Underfull \hbox (badness 6725) in paragraph at lines 11849--11858
\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/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 11849--11858
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 11849--11858
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2051]
Underfull \hbox (badness 3646) in paragraph at lines 11975--11977
[][][]$\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 /
[2052]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12013--12013
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[2053] [2054] [2055]
Underfull \hbox (badness 10000) in paragraph at lines 12194--12198
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12225--12231
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2056] [2057]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12401--12401
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[2058]
Underfull \hbox (badness 1009) in paragraph at lines 12419--12431
[]\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 12459--12461
[]\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
[2059]
Underfull \hbox (badness 1043) in paragraph at lines 12502--12507
[]\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
[2060] [2061] [2062] [2063]
Underfull \hbox (badness 1888) in paragraph at lines 12795--12798
[]\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 12812--12815
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2064]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12853--12853
[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
[2065]
Underfull \hbox (badness 2158) in paragraph at lines 12908--12911
[]\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 12956--12956
[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
[2066] [2067] [2068]
Underfull \hbox (badness 2302) in paragraph at lines 13113--13115
[]\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
[2069]
Underfull \hbox (badness 3333) in paragraph at lines 13220--13222
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2070] [2071] [2072]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 13387--13387
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
Underfull \hbox (badness 2012) in paragraph at lines 13411--13416
[]\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 have
Underfull \hbox (badness 5970) in paragraph at lines 13420--13423
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13420--13423
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2073]
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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-fault,
de-ter-min-ing the \T1/pcr/m/n/10 nlines \T1/ptm/m/n/10 ar-gu-ment to
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13479--13479
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2074]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13517--13517
[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13519--13519
[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[2075] [2076]
Underfull \hbox (badness 10000) in paragraph at lines 13687--13689
[]\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
[2077] [2078] [2079]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 13844--13851
\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$"\T1/ptm/m/n/10 ) and
[2080] [2081]
Underfull \hbox (badness 2020) in paragraph at lines 14013--14029
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 14013--14029
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2082] [2083]
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[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2084] [2085] [2086]
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[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
[2087] [2088] [2089] [2090] [2091] [2092]
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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
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.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 and \T
1/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 14826--14831
\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \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
[2093]
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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 av
ailable.packages(contriburl =
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\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
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
Underfull \hbox (badness 10000) in paragraph at lines 14891--14894
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2094]
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[]\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt")
[2095] [2096] [2097]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2098]
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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:[]
[2099]
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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)))[]
[2100] [2101]
Underfull \hbox (badness 1297) in paragraph at lines 15383--15385
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2102]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2103] [2104]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2105]
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[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15664--15666
[]\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 =
[2106] [2107] [2108]) [2109] [2110] (./KernSmooth-pkg.tex
Chapter 15.
[2111]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2112] [2113] [2114] [2115] [2116]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2117] [2118] [2119] [2120]) (./MASS-pkg.tex
Chapter 16.
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131]
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[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142]
[2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
[2154]
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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"),[]
[2155] [2156] [2157] [2158]
Underfull \hbox (badness 6559) in paragraph at lines 2698--2701
[]\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
[2159] [2160] [2161]
Underfull \hbox (badness 10000) in paragraph at lines 2868--2873
\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2868--2873
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\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 ,
[2162] [2163]
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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
[2164] [2165] [2166]
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[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
[2167]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178]
[2179]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2180] [2181] [2182] [2183] [2184] [2185] [2186]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4645--4645
[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[2187] [2188] [2189]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
[2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200]
[2201] [2202] [2203]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5918--5918
[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2204]
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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")
[2205] [2206]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6123 ...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.6123 ...sical N, P, K Factorial Experiment}{npk}
[2207]
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[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space.
That is
[2208] [2209] [2210] [2211]
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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)))[]
[2213]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2214] [2215] [2216] [2217] [2218] [2219]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7070--7070
[]\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"))[]
[2220]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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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 ) =
[2221]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2222] [2223]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2224] [2225]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2226]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2227] [2228] [2229] [2230] [2231] [2232]
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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
[2233] [2234]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8096--8096
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
Underfull \hbox (badness 1590) in paragraph at lines 8120--8124
[]\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
[2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245]
[2246] [2247] [2248] [2249] [2250] [2251] [2252] [2253] [2254]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9499--9499
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2255]
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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 ,
Underfull \hbox (badness 1158) in paragraph at lines 9626--9629
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2256]
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[]\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 9710--9710
[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9713--9713
[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2257] [2258] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267]
[2268] [2269]) (./Matrix-pkg.tex [2270]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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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
[2271]
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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
[2272]
Underfull \hbox (badness 2229) in paragraph at lines 159--162
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
Underfull \hbox (badness 1147) in paragraph at lines 159--162
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2273]
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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 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2274] [2275]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488
[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2276]
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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
Underfull \hbox (badness 4621) in paragraph at lines 512--516
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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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)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546
[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2277] [2278]
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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}"}.[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675
[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676
[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681
[]\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[]
[2279]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2280] [2281] [2282]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947
[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2283] [2284]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
[2285pdfTeX warning (ext4):
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2286]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266
[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2287]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1361--1361
[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
Underfull \hbox (badness 2277) in paragraph at lines 1389--1392
[]\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
[2288]
Underfull \hbox (badness 1609) in paragraph at lines 1436--1440
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2289]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1463--1463
[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1477--1477
[]\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[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1485--1485
[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
[2290]
Underfull \hbox (badness 10000) in paragraph at lines 1532--1539
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1532--1539
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1567--1571
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1583--1589
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2291]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1624 ... 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.1624 ... 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.1625 \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.1646 \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.1657 \aliasA{rowSums}{colSums}{rowSums}
[2292]
Underfull \hbox (badness 2922) in paragraph at lines 1711--1715
[]\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 1711--1715
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1722--1725
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2293] [2294]
Underfull \hbox (badness 3547) in paragraph at lines 1876--1879
[]\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
[2295] [2296] [2297] [2298] [2299]
Underfull \hbox (badness 1484) in paragraph at lines 2238--2240
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2300]
Underfull \hbox (badness 7379) in paragraph at lines 2334--2336
[]\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
[2301] [2302] [2303]
Underfull \hbox (badness 4846) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2615--2619
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2622--2625
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2304]
Underfull \hbox (badness 2689) in paragraph at lines 2678--2680
[]\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 2682--2687
[]\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 2682--2687
[][]\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
[2305]
Underfull \hbox (badness 1097) in paragraph at lines 2705--2708
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2718--2723
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2306]
Underfull \hbox (badness 3646) in paragraph at lines 2957--2960
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2989--2991
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 2992--2996
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 3001--3007
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2307]
Underfull \hbox (badness 10000) in paragraph at lines 3008--3012
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3018--3022
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2308] [2309]
Underfull \hbox (badness 10000) in paragraph at lines 3202--3204
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3249--3251
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2310]
Underfull \hbox (badness 2469) in paragraph at lines 3369--3372
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
, via
[2311] [2312]
Underfull \hbox (badness 10000) in paragraph at lines 3534--3538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3534--3538
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2313]
Underfull \hbox (badness 2285) in paragraph at lines 3584--3587
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2314] [2315]
Underfull \hbox (badness 10000) in paragraph at lines 3731--3736
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3731--3736
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3743--3746
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 :
if \T1/pcr/m/n/10 uplo ==
[2316]
Underfull \hbox (badness 10000) in paragraph at lines 3819--3821
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2317] [2318] [2319]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4029--4029
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 4097--4101
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
[2320]
Underfull \hbox (badness 10000) in paragraph at lines 4106--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4106--4109
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4111--4115
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
: the
[2321] [2322]
Underfull \hbox (badness 3158) in paragraph at lines 4294--4298
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2323] [2324] [2325] [2326]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4533--4533
[] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[]
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4536--4536
[] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4540--4540
[]\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 4543--4543
[]\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():[]
[2327] [2328] [2329] [2330]
Underfull \hbox (badness 10000) in paragraph at lines 4855--4860
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2331]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4936--4936
[]\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 4938--4938
[] \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 4942--4942
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2332]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4949--4949
[] \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 '[]
[2333] [2334]
Underfull \hbox (badness 4120) in paragraph at lines 5093--5096
[]\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 (15.18042pt too wide) in paragraph at lines 5130--5130
[]\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 5136--5136
[] \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 5137--5137
[] \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 5140--5140
[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5142--5142
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
[2335]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5149--5149
[]\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[]
[2336]
Underfull \hbox (badness 1817) in paragraph at lines 5241--5250
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 10000) in paragraph at lines 5283--5285
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5285--5288
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
Underfull \hbox (badness 1394) in paragraph at lines 5298--5301
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2337]
Underfull \hbox (badness 4765) in paragraph at lines 5316--5319
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2338]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5376--5376
[] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[]
[2339] [2340] [2341]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5634--5634
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[]
[2342]
Underfull \hbox (badness 10000) in paragraph at lines 5715--5718
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5726--5726
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2343]
Underfull \hbox (badness 1622) in paragraph at lines 5763--5768
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
\T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5763--5768
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2344]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5824--5824
[]\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 5825--5825
[] \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 5832--5832
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2345]
Underfull \hbox (badness 1062) in paragraph at lines 5961--5964
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2346]
Underfull \hbox (badness 6063) in paragraph at lines 5990--5993
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2347]
Underfull \hbox (badness 2635) in paragraph at lines 6102--6107
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6102--6107
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 6110--6113
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 6220--6230
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6220--6230
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2349]
Underfull \hbox (badness 3179) in paragraph at lines 6302--6305
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2350]
Underfull \hbox (badness 10000) in paragraph at lines 6400--6403
[]\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.,
[2351]
Underfull \hbox (badness 10000) in paragraph at lines 6475--6478
[]\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.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6491--6491
[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2352]
Underfull \hbox (badness 2443) in paragraph at lines 6530--6536
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6530--6536
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6551--6554
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2353]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6621--6621
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2354] [2355]
Underfull \hbox (badness 6268) in paragraph at lines 6757--6760
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
Underfull \hbox (badness 5036) in paragraph at lines 6781--6785
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
. How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6781--6785
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2356] [2357]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again>
\relax
l.6874 \aliasA{det}{Matrix-class}{det}
Underfull \hbox (badness 10000) in paragraph at lines 6977--6980
Underfull \hbox (badness 10000) in paragraph at lines 6987--6989
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2358]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.7050 ...*\%}{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.7158 ...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.7258 ...tcrossprod}{matrix-products}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 7356--7362
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2359] [2360pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7418 \end{Details}
pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7418 \end{Details}
]
Underfull \hbox (badness 10000) in paragraph at lines 7429--7432
[]\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 1199) in paragraph at lines 7429--7432
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 7432--7437
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 1371) in paragraph at lines 7432--7437
\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
Underfull \hbox (badness 1502) in paragraph at lines 7437--7441
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
Underfull \hbox (badness 10000) in paragraph at lines 7437--7441
\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
"dgeMatrix")\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 2837) in paragraph at lines 7447--7448
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2361] [2362]
Underfull \hbox (badness 1009) in paragraph at lines 7583--7585
[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
$\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
Underfull \hbox (badness 1062) in paragraph at lines 7628--7631
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2363]
Underfull \hbox (badness 6063) in paragraph at lines 7662--7665
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2364]
Underfull \hbox (badness 10000) in paragraph at lines 7714--7716
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2365] [2366]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7853--7853
[]\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 [2367]
Underfull \hbox (badness 2635) in paragraph at lines 7918--7923
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7918--7923
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7926--7929
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2368]
Underfull \hbox (badness 3482) in paragraph at lines 8000--8006
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
that these co-er-cions
[2369]
Underfull \hbox (badness 1867) in paragraph at lines 8120--8122
[]\T1/ptm/m/n/10 fast sim-
[2370]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8160 \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.8160 \HeaderA{norm}{Matrix Norms}{norm}
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8247--8247
[]\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 8248--8248
[]\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 8249--8249
[]\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 8362--8372
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2372]
Underfull \hbox (badness 3179) in paragraph at lines 8433--8436
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2373]
Underfull \hbox (badness 10000) in paragraph at lines 8523--8526
[]\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.,
[2374]
Underfull \hbox (badness 10000) in paragraph at lines 8599--8602
[]\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.,
[2375]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8615--8615
[]\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
Overfull \vbox (41.60564pt too high) has occurred while \output is active
[2376]
Underfull \hbox (badness 10000) in paragraph at lines 8725--8727
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
sig-na-tures (use
Underfull \hbox (badness 6493) in paragraph at lines 8727--8730
[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
Underfull \hbox (badness 6428) in paragraph at lines 8733--8740
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2377] [2378]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8826--8826
[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829
[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8831--8831
[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8835--8835
[]\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,[]
Underfull \hbox (badness 3989) in paragraph at lines 8861--8871
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8861--8871
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2379] [2380]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.8962 \aliasA{qr}{qr-methods}{qr}
[2381]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9035--9035
[]\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![]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9046--9046
[]\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 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[]
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[]\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[]
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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
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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/p
tm/m/n/10 , it cor-re-sponds to
[2383]
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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"[]
[2384]
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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![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.9258 ... the Reciprocal Condition Number}{rcond}
[2385] [2386]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9371--9371
[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2387] [2388]
Underfull \hbox (badness 10000) in paragraph at lines 9556--9558
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
via one di-men-sional
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\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
not
[2389] [2390]
Underfull \hbox (badness 1558) in paragraph at lines 9707--9710
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2391]
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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:[]
[2392]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9835 \aliasA{solve}{solve-methods}{solve}
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[] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9937--9937
[] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[]
[2393]
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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
Underfull \hbox (badness 10000) in paragraph at lines 9989--9992
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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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 : Checks
if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
[2394]
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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
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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
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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[][][]\T
1/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[]
[2395]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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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 con-t
rasts to be ap-plied to the
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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
[2396]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
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[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
\T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
be of-
[2397]
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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 10265--10265
[] \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 10266--10266
[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2398] [2399]
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[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
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[] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij =
FALSE)[]
[2400]
Underfull \hbox (badness 4621) in paragraph at lines 10491--10495
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2401]
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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[]
[2402]
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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)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10642--10642
[]\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"))) {[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10646--10646
[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2403]
Underfull \hbox (badness 10000) in paragraph at lines 10740--10748
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
[2404]
Underfull \hbox (badness 10000) in paragraph at lines 10791--10795
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.10831 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 10961--10963
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10989--10989
[] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
[2407]
Underfull \hbox (badness 2970) in paragraph at lines 11151--11157
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 11151--11157
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2408]
Underfull \hbox (badness 10000) in paragraph at lines 11224--11227
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2409]
Underfull \hbox (badness 10000) in paragraph at lines 11242--11247
[]\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 11257--11259
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2410] [2411]
Underfull \hbox (badness 2698) in paragraph at lines 11382--11388
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2412]
Underfull \hbox (badness 10000) in paragraph at lines 11475--11477
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
Underfull \hbox (badness 10000) in paragraph at lines 11493--11498
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11493--11498
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11501--11506
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2413]
Underfull \hbox (badness 2057) in paragraph at lines 11573--11575
[]\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.,
[2414] [2415]
Underfull \hbox (badness 6641) in paragraph at lines 11659--11662
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
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[]\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 11699--11703
\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
[2416]
Underfull \hbox (badness 7649) in paragraph at lines 11806--11808
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2417] [2418] [2419]
Underfull \hbox (badness 7362) in paragraph at lines 12007--12009
[]\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
[2420]
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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)[]
[2421] [2422]
Underfull \hbox (badness 6910) in paragraph at lines 12296--12298
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2423] [2424] [2425]) (./boot-pkg.tex [2426]
Chapter 18.
[2427] [2428] [2429] [2430] [2431] [2432] [2433]
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2434]
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
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[]\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-
[2435] [2436] [2437]
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 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2438]
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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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[2440]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
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\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply
\T1/pcr/m/n/10 "all"
[2441]
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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
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\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
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2442] [2443] [2444] [2445]
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-
[2446] [2447] [2448] [2449] [2450]
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),
[2451] [2452] [2453]
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[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2455]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2456] [2457] [2458]
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
[2459]
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$statis
tic \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 ,
[2460] [2461]
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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/10 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/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2462] [2463] [2464] [2465] [2466]
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[]\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,[]
[2467] [2468] [2469]
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.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2470]
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))
[2471] [2472] [2473]
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
[2474] [2475] [2476] [2477] [2478] [2479] [2480]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2481] [2482]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2483] [2484] [2485]
Underfull \hbox (badness 10000) in paragraph at lines 4190--4192
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2486]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2487] [2488]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4371--4375
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2489] [2490] [2491] [2492] [2493] [2494] [2495] [2496] [2497]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2498] [2499] [2500] [2501]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2502]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2503] [2504] [2505] [2506] [2507] [2508] [2509] [2510]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2511]
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 t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2512]
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 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2513] [2514] [2515] [2516]
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).
[2517] [2518]
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[]
[2519] [2520] [2521]
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
[2522] [2523]
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),[]
[2524] [2525] [2526] [2527] [2528] [2529] [2530] [2531]) (./class-pkg.tex
[2532]
Chapter 19.
[2533] [2534] [2535] [2536] [2537] [2538] [2539] [2540] [2541] [2542] [2543]
[2544] [2545] [2546] [2547] [2548]) (./cluster-pkg.tex
Chapter 20.
[2549]
Underfull \hbox (badness 1655) in paragraph at lines 134--143
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 134--143
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 134--143
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 134--143
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2550] [2551]
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]))[]
[2552] [2553]
Underfull \vbox (badness 10000) has occurred while \output is active [2554]
[2555]
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,
...)[]
[2556] [2557]
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)[]
[2558]
Underfull \hbox (badness 3078) in paragraph at lines 689--692
[]\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
[2559] [2560]
Underfull \hbox (badness 2941) in paragraph at lines 780--783
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 818--818
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2561]
Underfull \hbox (badness 10000) in paragraph at lines 865--867
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2562]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 930--930
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2563]
Underfull \hbox (badness 4872) in paragraph at lines 976--978
[]\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 990--994
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2564]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1104--1104
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2565]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1121--1121
[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1159--1159
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
[2566]
Underfull \hbox (badness 4144) in paragraph at lines 1191--1195
[]\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
[2567]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1267--1267
[] \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 1273--1273
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2568] [2569]
Underfull \hbox (badness 10000) in paragraph at lines 1412--1417
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 1460--1463
[2570]
Underfull \hbox (badness 10000) in paragraph at lines 1477--1481
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1501--1501
[]\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 1511--1511
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2571]
Underfull \hbox (badness 5741) in paragraph at lines 1551--1554
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2572]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1620--1620
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2573]
Underfull \hbox (badness 1540) in paragraph at lines 1737--1745
\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 =
[2574] [2575]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1828--1828
[]\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 1847--1847
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2576] [2577] [2578] [2579]
Underfull \hbox (badness 10000) in paragraph at lines 2166--2169
[2580]
Underfull \hbox (badness 3179) in paragraph at lines 2180--2186
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2581] [2582]
Underfull \hbox (badness 10000) in paragraph at lines 2338--2341
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2583]
Underfull \hbox (badness 1292) in paragraph at lines 2406--2409
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
Underfull \hbox (badness 6675) in paragraph at lines 2415--2417
[]\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 2438--2441
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2584] [2585] [2586] [2587]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2654--2654
[]\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 ):[]
[2588] [2589] [2590]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2923--2923
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2591] [2592]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3026--3026
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2593] [2594] [2595]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3222--3222
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3223--3223
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2596]
Underfull \hbox (badness 10000) in paragraph at lines 3290--3293
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2597]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3340--3340
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3341--3341
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2598] [2599] [2600]
Underfull \hbox (badness 10000) in paragraph at lines 3526--3529
[]\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
[2601]
Underfull \hbox (badness 10000) in paragraph at lines 3589--3594
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2602]
Underfull \hbox (badness 3884) in paragraph at lines 3651--3656
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3663--3666
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2603] [2604] [2605]
Underfull \hbox (badness 10000) in paragraph at lines 3848--3851
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3879--3882
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2606]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3932--3932
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 3943--3945
[]\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
[2607] [2608] [2609] [2610]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4136--4136
[] \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 4138--4138
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2611] [2612]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4276--4276
[]\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 4285--4285
[] \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 4287--4287
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
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[]\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 4292--4292
[] \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 4299--4299
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2613] [2614] [2615] [2616] [2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 4672--4678
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
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[]\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
[2619]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4701--4701
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
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[]\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[]
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[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
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[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2620]) (./codetools-pkg.tex
Chapter 21.
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[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
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[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
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[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2621]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2622]
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[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2623] [2624] [2625]) (./foreign-pkg.tex [2626]
Chapter 22.
[2627]
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
[2628] [2629]
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 ,
[2630]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2631] [2632] [2633]
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,[]
[2634]
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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-
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\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named
to
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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10
,
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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 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2635]
Underfull \hbox (badness 10000) in paragraph at lines 550--558
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 568--574
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2636]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623
[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
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[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2637]
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[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
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[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2638] [2639]
Underfull \hbox (badness 10000) in paragraph at lines 812--813
Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2640] [2641]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 900--900
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2642]
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[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2643] [2644]
Underfull \hbox (badness 10000) in paragraph at lines 1076--1077
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
format / data _ types .
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[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2645] [2646]
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 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2647]
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 side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2648]) (./lattice-pkg.tex
Chapter 23.
[2649]
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 /
[2650] [2651]
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"),[]
[2652]
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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"),[]
[2653] [2654] [2655] [2656]
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
[2657] [2658] [2659] [2660]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2661]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2662] [2663]
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
[2664] [2665] [2666]
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 ,
[2667]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2668]
Underfull \vbox (badness 10000) has occurred while \output is active [2669]
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
[2670]
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\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
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
[2671] [2672] [2673] [2674]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
[2675]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2676] [2677] [2678]
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"),[]
[2679] [2680] [2681] [2682] [2683]
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"),[]
[2684] [2685]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2686]
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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 2888--2892
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2894--2896
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
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[]\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,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2970--2974
[]\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
[2687] [2688]
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[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
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[] \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 3075--3075
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3086--3086
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
[2689]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
Underfull \hbox (badness 2913) in paragraph at lines 3156--3163
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3156--3163
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2690] [2691] [2692] [2693]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3444 \aliasA{parallel}{B\_08\_splom}{parallel}
[2694]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3509--3509
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2695] [2696] [2697] [2698] [2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3845--3845
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2700]
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[]\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
[2701] [2702]
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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
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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
[2703]
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\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4183--4187
\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
[2704] [2705]
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
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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 ,
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\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
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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 f
or \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 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
[2706]
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4325--4327
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2707] [2708] [2709] [2710] [2711]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4729--4729
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2712] [2713]
Underfull \hbox (badness 10000) in paragraph at lines 4916--4919
[]\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 .
[2714] [2715]
Underfull \hbox (badness 1442) in paragraph at lines 5048--5051
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2716] [2717] [2718] [2719] [2720] [2721]
Underfull \hbox (badness 3646) in paragraph at lines 5382--5385
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5412--5412
[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5413--5413
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2722]
Underfull \hbox (badness 10000) in paragraph at lines 5501--5504
[]\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 5501--5504
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2723]
Underfull \hbox (badness 1635) in paragraph at lines 5527--5532
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2724]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5678--5678
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2725]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5692--5692
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5693--5693
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5696--5696
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5699--5699
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5701--5701
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5707--5707
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5708--5708
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5709--5709
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5710--5710
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5711--5711
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5727--5729
[]\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 5738--5740
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2726] [2727]
Underfull \hbox (badness 2538) in paragraph at lines 5863--5867
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5874--5881
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5874--5881
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2728] [2729]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6031
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2730] [2731]
Underfull \hbox (badness 4242) in paragraph at lines 6174--6179
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2732] [2733]
Underfull \hbox (badness 3601) in paragraph at lines 6290--6295
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6290--6295
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2734]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6377--6377
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2735] [2736]
Underfull \hbox (badness 1888) in paragraph at lines 6509--6516
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2737]
Underfull \hbox (badness 10000) in paragraph at lines 6566--6569
[]\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 6566--6569
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2738] [2739] [2740] [2741] [2742] [2743]
Underfull \hbox (badness 1320) in paragraph at lines 6972--6979
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6972--6979
\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
[2744]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7042--7042
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2745]
Underfull \hbox (badness 10000) in paragraph at lines 7072--7076
[]\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 7072--7076
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 7177--7180
\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
[2747] [2748]
Underfull \hbox (badness 2012) in paragraph at lines 7343--7346
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2749]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7389--7389
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2750] [2751]
Underfull \hbox (badness 2644) in paragraph at lines 7530--7534
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7543--7546
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
[2752]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7613--7613
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7623--7623
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2753]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7684--7684
[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7689--7689
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2754] [2755] [2756]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7874--7874
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2757]
Underfull \hbox (badness 1436) in paragraph at lines 7929--7935
[]\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
[2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765]
Underfull \hbox (badness 10000) in paragraph at lines 8487--8490
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8487--8490
\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
[2766] [2767]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8662--8662
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8663--8663
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8675--8675
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2768]
Underfull \hbox (badness 3118) in paragraph at lines 8694--8697
[]\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
[2769]
Underfull \hbox (badness 1515) in paragraph at lines 8770--8774
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2770]
Underfull \hbox (badness 6316) in paragraph at lines 8876--8881
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2771] [2772]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8983--8983
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2773] [2774]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9122--9122
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2775]
Overfull \hbox (42.94879pt too wide) in paragraph at lines 9181--9185
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
Overfull \hbox (50.63074pt too wide) in paragraph at lines 9181--9185
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2776] [2777] [2778] [2779] [2780] [2781] [2782]
Underfull \hbox (badness 7238) in paragraph at lines 9639--9643
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9639--9643
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2783] [2784] [2785]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9870 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2786] [2787] [2788]
Underfull \hbox (badness 10000) in paragraph at lines 10032--10037
\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 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10105--10105
[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2789] [2790]) (./mgcv-pkg.tex
Chapter 24.
[2791] [2792]
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,[]
[2793]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 165--165
[] \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
Underfull \hbox (badness 1043) in paragraph at lines 209--214
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2794] [2795] [2796] [2797]
Underfull \hbox (badness 10000) in paragraph at lines 378--385
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 378--385
[][]\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 378--385
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2798]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 421--421
[]\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)+[]
[2799] [2800] [2801]
Underfull \hbox (badness 2922) in paragraph at lines 633--634
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2802] [2803]
Underfull \hbox (badness 2205) in paragraph at lines 703--704
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-i
ng evi-ron-ment vari-able
[2804] [2805]
Underfull \hbox (badness 1158) in paragraph at lines 813--815
[]\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
[2806]
Underfull \hbox (badness 1259) in paragraph at lines 876--877
[]\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).
[2807]
Underfull \vbox (badness 10000) has occurred while \output is active [2808]
[2809] [2810] [2811] [2812]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1224--1224
[]\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 1225--1225
[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1231--1231
[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1238--1238
[]\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
this stratum...[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1240--1240
[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242
[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
[2813]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1273--1273
[]\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)[]
[2814]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1334--1334
[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
[2815]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1345--1345
[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1379--1379
[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
[2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1882--1882
[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2824] [2825] [2826] [2827] [2828] [2829] [2830]
Underfull \hbox (badness 1052) in paragraph at lines 2270--2278
\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
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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/1
0 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
[2831]
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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.
[2832] [2833] [2834]
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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
[2835]
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[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
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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 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
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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)),[]
[2848] [2849] [2850] [2851] [2852] [2853]
Underfull \hbox (badness 5189) in paragraph at lines 3659--3663
[]\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
[2854]
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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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[2857]
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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)+[]
[2866] [2867]
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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,
[2868] [2869]
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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
[2870]
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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-genc
e fail-ures, con-sider mod-i-fy-ing
[2871] [2872]
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[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2873]
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[2875] [2876] [2877] [2878]
Underfull \hbox (badness 1577) in paragraph at lines 5208--5211
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2879] [2880] [2881] [2882] [2883] [2884] [2885]
Underfull \hbox (badness 6708) in paragraph at lines 5604--5605
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2886]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
[2887]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
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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[]
[2889] [2890] [2891] [2892] [2893]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
[2894]
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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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[2899]
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[]\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2)
[2900]
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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)
[2901] [2902] [2903] [2904]
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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)[]
[2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917]
Underfull \hbox (badness 1242) in paragraph at lines 7436--7437
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2918] [2919]
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2920]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
[2921]
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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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[2933] [2934] [2935] [2936] [2937] [2938] [2939]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8825--8828
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 8825--8828
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2941]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 8881--8884
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
be
[2942] [2943] [2944] [2945]
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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,[]
[2946] [2947]
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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
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[2951]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[]
[2952]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para-
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\T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c
luded terms,
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
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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[]
[2959]
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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
[2960]
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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
[2961]
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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-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2962] [2963]
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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,
[2964] [2965] [2966] [2967]
Underfull \hbox (badness 1946) in paragraph at lines 10417--10424
[]\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: s
ee
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
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\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2968]
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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)[]
[2969]
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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 ,
[2970] [2971] [2972] [2973] [2974]
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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)
[2975] [2976] [2977] [2978] [2979]
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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,[]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2981]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
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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
[2984] [2985]
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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 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
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\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
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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/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2986] [2987] [2988]
Underfull \hbox (badness 6876) in paragraph at lines 11681--11687
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
or two vari-ables, spec-i-fied via terms like
[2989]
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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
[2990] [2991]
Underfull \hbox (badness 10000) in paragraph at lines 11839--11840
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2992] [2993]
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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)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11917--11917
[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11922--11922
[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11928--11928
[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11929--11929
[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[2994]
Underfull \hbox (badness 10000) in paragraph at lines 11998--12000
[]\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 11998--12000
\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
[2995] [2996] [2997]
Underfull \hbox (badness 10000) in paragraph at lines 12126--12127
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2998]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12207--12207
[]\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 12208--12208
[]\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[]
[2999] [3000] [3001]
Underfull \hbox (badness 10000) in paragraph at lines 12358--12359
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3002] [3003] [3004] [3005]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12597--12597
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3006]
Underfull \hbox (badness 10000) in paragraph at lines 12658--12660
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3007] [3008] [3009]
Underfull \hbox (badness 10000) in paragraph at lines 12817--12820
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 12817--12820
\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 12817--12820
\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"
[3010]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12901--12901
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3011]
Underfull \hbox (badness 10000) in paragraph at lines 12946--12952
[]\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 12946--12952
\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-
[3012] [3013] [3014]
Underfull \vbox (badness 10000) has occurred while \output is active [3015]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13160--13160
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
Underfull \vbox (badness 10000) has occurred while \output is active [3016]
Underfull \hbox (badness 10000) in paragraph at lines 13263--13271
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
[3017]
Underfull \hbox (badness 10000) in paragraph at lines 13289--13290
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3018] [3019] [3020] [3021]
Underfull \hbox (badness 3396) in paragraph at lines 13550--13553
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
num-ber of vari-ables, spec-i-fied via terms like
[3022]
Underfull \hbox (badness 10000) in paragraph at lines 13595--13597
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3023] [3024] [3025] [3026]
Underfull \hbox (badness 10000) in paragraph at lines 13819--13822
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 13819--13822
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 13852--13856
[][][]\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 13852--13856
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13852--13856
[][]\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 ,
[3027] [3028] [3029] [3030] [3031]
Underfull \hbox (badness 2158) in paragraph at lines 14142--14142
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3032] [3033]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14221--14221
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3034] [3035]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14355--14355
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3036] [3037]
Underfull \hbox (badness 4846) in paragraph at lines 14486--14489
[]\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
[3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048]
[3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15682--15682
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[3058] [3059] [3060]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 15892--15892
[]\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,
[3061]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15894--15894
[]\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 15896--15896
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
Underfull \hbox (badness 10000) in paragraph at lines 15915--15916
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 15915--15916
\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected
by \T1/pcr/m/n/10 ar.row
[3062] [3063] [3064]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16040--16040
[]\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 16041--16041
[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16053--16053
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[3065] [3066] [3067]) (./nlme-pkg.tex [3068]
Chapter 25.
[3069]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3070]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3071] [3072] [3073] [3074] [3075]
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,[]
[3076] [3077]
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 ---------------------------
---------------[]
[3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085]
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"),[]
[3086]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3087] [3088] [3089] [3090] [3091] [3092] [3093]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3094]
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
[3095] [3096] [3097] [3098] [3099]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3100]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[3101]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3102] [3103]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3104]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123]
[3124]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134] [3135]
[3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146]
[3147] [3148]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3149] [3150] [3151] [3152] [3153] [3154] [3155]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\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 ,
[3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\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
[3165]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\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 ,
[3166]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3167]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3168] [3169] [3170] [3171]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\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 ,
[3172]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3173]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3174]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3175] [3176] [3177]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3178]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3179] [3180] [3181]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3182] [3183] [3184]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7406--7414
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7429--7432
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3185] [3186] [3187]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\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
[3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3196] [3197] [3198] [3199] [3200]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3201]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.8572 \aliasA{sigma}{lmeObject}{sigma}
[3202] [3203] [3204] [3205] [3206]
[3207] [3208] [3209] [3210] [3211] [3212] [3213]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3214]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3215] [3216] [3217] [3218]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9686 ...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.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3219]
Underfull \hbox (badness 10000) in paragraph at lines 9706--9709
[]\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 9750--9753
[]\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 9750--9753
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3228] [3229] [3230]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3231]
Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3232] [3233] [3234]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3235] [3236]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3237]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10838--10840
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3238] [3239] [3240] [3241]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
[]\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 11131--11131
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
[3242] [3243] [3244] [3245] [3246] [3247]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11521--11521
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3248] [3249] [3250] [3251] [3252] [3253]
Underfull \hbox (badness 6268) in paragraph at lines 11908--11918
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3254] [3255] [3256] [3257]
Underfull \hbox (badness 10000) in paragraph at lines 12169--12175
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3258] [3259] [3260] [3261] [3262]
Underfull \hbox (badness 6876) in paragraph at lines 12491--12493
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
\T1/ptm/m/n/10 will be con-structed from
[3263] [3264]
Underfull \hbox (badness 2452) in paragraph at lines 12647--12654
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3265]
Underfull \hbox (badness 10000) in paragraph at lines 12712--12718
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13301--13301
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3275] [3276] [3277] [3278] [3279]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13666--13666
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3280]
Underfull \hbox (badness 10000) in paragraph at lines 13693--13696
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3281]
Underfull \hbox (badness 1838) in paragraph at lines 13736--13743
[]\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 13736--13743
\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 13793--13793
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3282]
Underfull \hbox (badness 10000) in paragraph at lines 13800--13803
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13800--13803
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13828--13831
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13828--13831
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3283]
Underfull \hbox (badness 10000) in paragraph at lines 13908--13911
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3284]
Underfull \hbox (badness 1472) in paragraph at lines 13933--13940
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3285]
Underfull \hbox (badness 10000) in paragraph at lines 14002--14004
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3286] [3287] [3288] [3289]
Underfull \hbox (badness 1215) in paragraph at lines 14282--14284
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3290] [3291] [3292] [3293]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14526--14526
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302]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.15179 ...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.15179 ...Extract Random Effects}{random.effects}
[3303] [3304] [3305]
[3306] [3307] [3308] [3309] [3310] [3311] [3312] [3313]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15827--15827
[]\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 15846--15846
[] \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 15847--15847
[] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),
tol = 7e-7)[]
[3314]
Underfull \hbox (badness 1009) in paragraph at lines 15877--15886
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3315] [3316]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16024--16024
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3317] [3318] [3319] [3320] [3321]
Underfull \hbox (badness 10000) in paragraph at lines 16359--16365
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3322]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16390--16390
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3323] [3324] [3325] [3326] [3327] [3328] [3329]
Underfull \hbox (badness 1728) in paragraph at lines 16879--16882
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3330] [3331] [3332] [3333] [3334]
Underfull \hbox (badness 1867) in paragraph at lines 17214--17223
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple 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 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3335]
Underfull \hbox (badness 1521) in paragraph at lines 17278--17286
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance
Underfull \hbox (badness 10000) in paragraph at lines 17278--17286
\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 1694) in paragraph at lines 17278--17286
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3336] [3337] [3338] [3339]
Underfull \hbox (badness 10000) in paragraph at lines 17525--17532
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3340] [3341] [3342] [3343] [3344] [3345] [3346]
Underfull \hbox (badness 10000) in paragraph at lines 18060--18070
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18060--18070
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3347]
Underfull \hbox (badness 3579) in paragraph at lines 18098--18103
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3348]
Underfull \hbox (badness 3579) in paragraph at lines 18162--18167
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3349]
Underfull \hbox (badness 3579) in paragraph at lines 18225--18230
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3350]
Underfull \hbox (badness 1577) in paragraph at lines 18286--18288
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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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/ptm/m
/n/10 , in which case a se-quence
[3351]
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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/ptm/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 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3352]
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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/ptm/m
/n/10 , in which case a se-quence
[3353] [3354]
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\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3355] [3356]
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\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365]) (./nnet-pkg.tex
[3366]
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}
[3367]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3368] [3369] [3370]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3371]
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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)[]
[3372] [3373]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3374]) (./rpart-pkg.tex
Chapter 27.
[3375] [3376] [3377] [3378]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3379] [3380] [3381] [3382]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3383] [3384]
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[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3385] [3386]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3387]
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[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3388] [3389] [3390]
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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, ...)[]
[3391]
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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/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3392]
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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,[]
[3393] [3394] [3395] [3396] [3397] [3398]
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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 ',
[3399] [3400]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3401] [3402] [3403]) (./spatial-pkg.tex [3404]
Chapter 28.
[3405] [3406] [3407] [3408] [3409] [3410]
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[3411] [3412] [3413] [3414] [3415] [3416] [3417] [3418] [3419] [3420] [3421]
[3422] [3423]) (./survival-pkg.tex [3424]
Chapter 29.
[3425] [3426]
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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.[]
[3427] [3428]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again>
\relax
l.326 ... 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.326 ... Myelogenous Leukemia survival data}{aml}
[3429] [3430]
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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)[]
[3431]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3432] [3433]
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[]\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size,
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3435] [3436]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3437] [3438] [3439]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\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[]
[3440] [3441]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3442]
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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.1177 ...erapy for Stage B/C colon cancer}{colon}
[3443]
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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, ...)[]
[3444] [3445]
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[] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[]
[3446]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3447] [3448] [3449] [3450]
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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:: \T1/pt
m/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(t
ime,status) ~ age +
[3451]
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[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.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 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3452]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3461] [3462] [3463]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3464] [3465] [3466] [3467]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3468]
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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"),[]
[3469] [3470]
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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 )))[]
[3471] [3472]
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[] []
[3473] [3474] [3475]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3476] [3477] [3478] [3479] [3480]
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[] \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 )))[]
[3481] [3482] [3483] [3484]
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[3486] [3487]
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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,[]
[3488] [3489] [3490]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3491]
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[]\T1/pcr/m/n/9 mresid <- (lung$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[]
[3492]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3493]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3494] [3495]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3496] [3497]
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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, ...)[]
[3498] [3499] [3500]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3501]
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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)) +[]
[3502] [3503] [3504] [3505] [3506]
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[3508] [3509]
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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/ptm/m/n/10
, \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3510] [3511] [3512] [3513] [3514]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.6186 ...ata from a soldering experiment}{solder}
[3515] [3516]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3517] [3518] [3519] [3520] [3521]
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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,[]
[3522] [3523] [3524] [3525]
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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 ),[]
[3526] [3527] [3528]
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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 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3529]
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[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3530] [3531] [3532]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
form
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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample
test, the
[3533]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
[3534]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3535]
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3536]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3537] [3538] [3539]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
[3540]
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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"),[]
[3541] [3542]
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[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3543] [3544]
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[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
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\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
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\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
[3545]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3546] [3547] [3548] [3549] [3550]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3551]
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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
[3552] [3553]
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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 surv
reg.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 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 9052--9059
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3554]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3555] [3556] [3557]
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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 )[]
[3558] [3559]
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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 )[]
[3560] [3561] [3562] [3563]
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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[]
[3564]
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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)[]
[3565] [3566] [3567] [3568] [3569] [3570] [3571]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3572] [3573] [3574]) (./fullrefman.ind [3575] [3576] [3577] [3578] [3579]
[3580] [3581] [3582] [3583] [3584] [3585] [3586] [3587] [3588] [3589] [3590]
[3591] [3592] [3593] [3594] [3595] [3596] [3597] [3598]
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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.bs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
[3599]
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[]| \T1/pcr/m/n/10 smooth.construct.ps.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.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 ,
[3600] [3601] [3602] [3603] [3604]
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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.bs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
[3605]
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ps.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.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 ,
[3606]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
[3607] [3608] [3609] [3610] [3611] [3612] [3613] [3614] [3615]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method
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[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method
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[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method
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[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method
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[]\T1/pcr/m/n/10 [,dMatrix,lMatrix,missing,ANY-method
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[]\T1/pcr/m/n/10 [,dMatrix,logical,missing,ANY-method
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[]\T1/pcr/m/n/10 [,denseMatrix,index,index,logical-method
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[]\T1/pcr/m/n/10 [,denseMatrix,missing,index,logical-method
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[]\T1/pcr/m/n/10 [,diagonalMatrix,index,index,logical-method
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[]\T1/pcr/m/n/10 [,diagonalMatrix,index,missing,logical-method
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[]\T1/pcr/m/n/10 [,diagonalMatrix,missing,index,logical-method
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[]\T1/pcr/m/n/10 [,indMatrix,index,missing,logical-method
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[]\T1/pcr/m/n/10 [,sparseMatrix,missing,index,logical-method
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[]\T1/pcr/m/n/10 [,sparseVector,index,ANY,ANY-method
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[]\T1/pcr/m/n/10 [,sparseVector,lsparseVector,ANY,ANY-method
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[]\T1/pcr/m/n/10 [,sparseVector,nsparseVector,ANY,ANY-method
[3616]
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,Matrix,missing,replValue-method
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,replValue-method
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,sparseVector-method
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[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ldenseMatrix,missing,replValue-method
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[3617]
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\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
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[3647]
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[3648]
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[3701] [3702] [3703]
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[]\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-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
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[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method
[3706]
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[]\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method
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[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method
[3707] [3708] [3709] [3710] [3711]
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method
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[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method
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[3716]
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[]\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method
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[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method
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Chapter 1.
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
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[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
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rel.diff.=",[]
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
[16] [17] [18] [19] [20]
Underfull \hbox (badness 1838) in paragraph at lines 1200--1203
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[21] [22] [23] [24] [25] [26]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1710--1710
[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
[27]
Underfull \hbox (badness 1303) in paragraph at lines 1738--1741
[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
than 256 (or
[28] [29]
Underfull \hbox (badness 10000) in paragraph at lines 1856--1858
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
[30] [31]
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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 tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[32] [33] [34] [35]
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[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
[36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2431--2433
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
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[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[38]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[39] [40]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2669--2669
[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3337--3337
[]\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",[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3369--3369
[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
[51]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3376--3376
[]\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 3377--3377
[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3380--3380
[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
[52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3820--3822
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 4061--4061
[] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive)
[62] [63] [64]
Underfull \hbox (badness 4927) in paragraph at lines 4319--4323
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
Underfull \hbox (badness 2012) in paragraph at lines 4319--4323
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[65] [66]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4403--4403
[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
[67]
Underfull \hbox (badness 4595) in paragraph at lines 4468--4471
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4626--4626
[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4651--4651
[] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e
xclude = TRUE)[]
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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
[70] [71] [72]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4844--4844
[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5097--5099
[]\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
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5509--5517
[]\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
[82] [83] [84] [85] [86] [87] [88] [89] [90]
Underfull \hbox (badness 1796) in paragraph at lines 6075--6083
[]\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 : / /
[91] [92]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6269--6269
[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 6271--6271
[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6272--6272
[]\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}[]
[93] [94]
Underfull \hbox (badness 1242) in paragraph at lines 6411--6415
\T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel
ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment.
[95]
Underfull \hbox (badness 1635) in paragraph at lines 6474--6477
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
Underfull \hbox (badness 3009) in paragraph at lines 6478--6481
[]\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
[96]
Underfull \hbox (badness 1308) in paragraph at lines 6521--6529
[]\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
[97] [98]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6685--6685
[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
Underfull \vbox (badness 10000) has occurred while \output is active [99]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6735--6737
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 :
[100]
Underfull \hbox (badness 1997) in paragraph at lines 6862--6867
[]\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1
0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x
zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC
onnection\T1/ptm/m/n/10 ,
[101]
Underfull \hbox (badness 10000) in paragraph at lines 6900--6903
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 6900--6903
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[102] [103]
Underfull \hbox (badness 1406) in paragraph at lines 7082--7088
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
Underfull \hbox (badness 2173) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and
web-pages gen-er-ated by
Underfull \hbox (badness 2134) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 7082--7088
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 7102--7104
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[104]
Underfull \hbox (badness 1067) in paragraph at lines 7144--7151
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[105] [106]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 7346--7346
[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
[108] [109]
Underfull \hbox (badness 1231) in paragraph at lines 7471--7477
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the
first el-e-
[110] [111] [112]
Underfull \hbox (badness 10000) in paragraph at lines 7683--7685
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[113] [114]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7828--7828
[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
[115] [116] [117] [118]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8066--8066
[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
[119] [120]
Underfull \hbox (badness 10000) in paragraph at lines 8188--8198
[]\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 8188--8198
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
is a generic func-tion, meth-ods can be
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8220--8225
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[121] [122] [123] [124] [125] [126] [127]
Underfull \hbox (badness 1629) in paragraph at lines 8709--8721
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8709--8721
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
, and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[128] [129] [130] [131] [132] [133]
Underfull \hbox (badness 10000) in paragraph at lines 9157--9161
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[134]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9248--9248
[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9250--9250
[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
[135]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9276--9276
[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9277--9277
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
[136] [137]
Underfull \hbox (badness 5403) in paragraph at lines 9414--9416
[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9433--9435
[]\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
[138] [139] [140]
Underfull \hbox (badness 1603) in paragraph at lines 9658--9661
[]\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
[141] [142] [143] [144] [145] [146] [147] [148] [149]
Underfull \hbox (badness 1917) in paragraph at lines 10266--10271
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[150]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10321--10321
[]\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 10322--10322
[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
[151] [152]
Underfull \hbox (badness 1168) in paragraph at lines 10424--10429
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
Underfull \hbox (badness 10000) in paragraph at lines 10463--10469
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
Underfull \hbox (badness 5403) in paragraph at lines 10470--10473
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[153] [154]
Underfull \hbox (badness 2828) in paragraph at lines 10629--10633
[][][]$\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 10629--10633
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / Double _
[155]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10662--10662
[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
[156]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10735--10735
[]\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, ..[]
[157] [158]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10882--10882
[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
[159] [160] [161]
Underfull \hbox (badness 6396) in paragraph at lines 11079--11087
[]\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 11088--11090
[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[162] [163] [164]
Underfull \hbox (badness 10000) in paragraph at lines 11305--11308
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[165] [166] [167] [168] [169] [170] [171] [172] [173]
Underfull \hbox (badness 5288) in paragraph at lines 12007--12009
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
[174]
Underfull \hbox (badness 3039) in paragraph at lines 12017--12022
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
and
Underfull \hbox (badness 10000) in paragraph at lines 12077--12079
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[175] [176]
Underfull \hbox (badness 4569) in paragraph at lines 12199--12203
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
passed as an ar-gu-ment
Underfull \hbox (badness 2401) in paragraph at lines 12199--12203
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[177] [178]
Underfull \hbox (badness 10000) in paragraph at lines 12314--12316
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13159--13159
[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
[190] [191] [192] [193] [194] [195]
Underfull \hbox (badness 2221) in paragraph at lines 13609--13618
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
Underfull \hbox (badness 1635) in paragraph at lines 13609--13618
\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[196] [197] [198] [199]
Underfull \hbox (badness 2253) in paragraph at lines 13870--13872
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
[200] [201]
Underfull \hbox (badness 2573) in paragraph at lines 13987--13989
[]\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 =
[202] [203]
Underfull \hbox (badness 10000) in paragraph at lines 14142--14144
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[204] [205]
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14270--14273
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \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[]
[206]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
[207]
Underfull \hbox (badness 10000) in paragraph at lines 14410--14413
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14420--14420
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[208]
Underfull \hbox (badness 10000) in paragraph at lines 14486--14489
[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
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:[]
[209]
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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 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14556--14563
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14564--14568
[]\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,
[210] [211] [212]
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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)[]
[213] [214] [215]
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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[]
[216]
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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
[217]
Underfull \hbox (badness 6944) in paragraph at lines 15146--15149
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[218]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15171--15171
[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
[219] [220]
Underfull \hbox (badness 10000) in paragraph at lines 15309--15311
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
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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)),[]
[221]
Underfull \hbox (badness 2790) in paragraph at lines 15342--15345
[]\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
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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
[222]
Underfull \hbox (badness 10000) in paragraph at lines 15448--15450
[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls
Underfull \hbox (badness 4954) in paragraph at lines 15448--15450
\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
in this
Underfull \hbox (badness 10000) in paragraph at lines 15470--15475
[]\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/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-rides
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
[223]
Underfull \hbox (badness 10000) in paragraph at lines 15482--15486
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
Underfull \hbox (badness 10000) in paragraph at lines 15482--15486
\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 15487--15495
[]\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
[224]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15595--15595
[]\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[]
[226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16435--16435
[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
[238]
Underfull \hbox (badness 2418) in paragraph at lines 16544--16548
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
,
Underfull \hbox (badness 6510) in paragraph at lines 16551--16554
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
[239]
Underfull \hbox (badness 2326) in paragraph at lines 16586--16593
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[240] [241] [242]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16836--16836
[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
[243]
Underfull \hbox (badness 1867) in paragraph at lines 16861--16868
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[244] [245] [246] [247]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17139--17139
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
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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 17219--17219
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
[249] [250] [251] [252]
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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)))
[253]
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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"))[]
[254] [255] [256]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17841--17841
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
[257] [258] [259] [260]
Underfull \hbox (badness 2435) in paragraph at lines 18109--18111
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
. unicode . org / reports / tr35 /
[261]
Underfull \hbox (badness 2285) in paragraph at lines 18175--18177
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
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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.[]
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[] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
[262] [263]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
[264]
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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" :[]
[265] [266]
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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):[]
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 18702--18704
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[270] [271] [272] [273] [274] [275] [276] [277]
Underfull \hbox (badness 4699) in paragraph at lines 19275--19278
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[278] [279]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19403--19403
[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
[280] [281]
Underfull \hbox (badness 4739) in paragraph at lines 19538--19540
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[282]
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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)[]
[283] [284] [285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1975) in paragraph at lines 20166--20169
[]\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
[291] [292] [293] [294] [295] [296]
Underfull \hbox (badness 1077) in paragraph at lines 20564--20569
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
[297]
Underfull \hbox (badness 10000) in paragraph at lines 20578--20585
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
\T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[298]
Underfull \hbox (badness 10000) in paragraph at lines 20652--20656
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[299] [300]
Underfull \hbox (badness 10000) in paragraph at lines 20801--20805
[]\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 20801--20805
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 20806--20813
[]\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-
[301] [302]
Underfull \hbox (badness 10000) in paragraph at lines 20937--20944
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[303]
Underfull \hbox (badness 10000) in paragraph at lines 21058--21062
[]\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
[304]
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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 21128--21133
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 21128--21133
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion
3 of the li-cense can be dis-played by
[305] [306] [307]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
[308]
Underfull \hbox (badness 3343) in paragraph at lines 21360--21364
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
many more file han-dling func-tions and
[309] [310]
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[] \T1/pcr/m/n/9 identical(L$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,
pr = 0.2))),[]
[311] [312]
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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-
[313]
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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
[314]
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[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
[315] [316]
Underfull \hbox (badness 1400) in paragraph at lines 21958--21962
[][][]\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 do
uble[][][] \T1/ptm/m/n/10 (class
[317] [318] [319]
Underfull \hbox (badness 2469) in paragraph at lines 22128--22134
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
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\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
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\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[320] [321] [322] [323] [324] [325] [326] [327] [328]
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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 ))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 22770--22770
[]\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)[]
[329] [330]
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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'):
[331] [332] [333] [334]
Underfull \hbox (badness 2277) in paragraph at lines 23143--23146
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
\T1/ptm/m/n/10 are typ-i-cally prefer-able.
[335] [336]
Underfull \hbox (badness 10000) in paragraph at lines 23272--23275
[]\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc
r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.
0,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 1484) in paragraph at lines 23724--23732
[]\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 /
[343] [344]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 23802--23802
[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
[345] [346] [347] [348] [349] [350] [351]
Underfull \hbox (badness 1448) in paragraph at lines 24310--24318
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[352] [353]
Underfull \hbox (badness 3849) in paragraph at lines 24425--24430
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[354]
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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-re-spond-
ing
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\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE))
\T1/ptm/m/n/10 which are also given by
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[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10
. If the en-vi-ron-ment is used as a hash
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[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute
via the gen-eral rules:
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\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[355] [356]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[357] [358] [359]
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[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[360] [361] [362]
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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-
[363] [364] [365] [366] [367]
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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-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
Underfull \hbox (badness 2846) in paragraph at lines 25394--25398
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the
pack-
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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 com-p
uted 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)
[368]
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
[369]
Underfull \hbox (badness 10000) in paragraph at lines 25488--25494
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 25488--25494
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
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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:[]
[370] [371] [372]
Underfull \hbox (badness 8189) in paragraph at lines 25747--25753
[]\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
[][][]
[373] [374] [375]
Underfull \hbox (badness 1694) in paragraph at lines 25972--25975
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
(see `De-tails');
[376] [377] [378] [379]
Underfull \hbox (badness 1603) in paragraph at lines 26219--26221
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[380] [381]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 26346--26354
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[382] [383]
Underfull \hbox (badness 3271) in paragraph at lines 26565--26568
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[384] [385] [386]
Underfull \hbox (badness 3138) in paragraph at lines 26865--26871
[]\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 26865--26871
\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 26865--26871
\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 26878--26881
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
and
[387]
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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
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[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
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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
[388]
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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 26981--26987
\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 26981--26987
\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 26981--26987
\T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina
ry.universal" \T1/ptm/m/n/10 are no longer
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[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
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\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
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\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 26996--27003
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[389] [390] [391] [392]
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[]\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 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
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\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[394] [395]
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[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
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\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[396] [397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27782--27788
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
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[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
\T1/ptm/m/n/10 which con-cate-nates and
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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[]
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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)[]
[400] [401] [402]
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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 =
[403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1817) in paragraph at lines 28379--28383
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m
/n/10 get[][][](name,envir =
[409]
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[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
see
[410] [411] [412]
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[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[413] [414] [415] [416] [417] [418] [419] [420] [421] [422]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 29343--29343
[] \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))[]
[423] [424]
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[426]
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[]\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"[]
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[]\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 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
Underfull \vbox (badness 10000) has occurred while \output is active [427]
[428]
Underfull \hbox (badness 7415) in paragraph at lines 29725--29729
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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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[]
[429]
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[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
[430]
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[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[431] [432]
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\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 30059--30066
\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 /
[433] [434]
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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
[435] [436]
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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 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[437] [438]
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[]\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")[]
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[]\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")[]
[439]
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[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
[440] [441] [442] [443] [444]
Underfull \hbox (badness 4048) in paragraph at lines 30843--30848
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
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\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 ,
[445] [446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 2080) in paragraph at lines 31380--31390
[]\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.[]
[453] [454] [455] [456] [457] [458] [459]
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[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 31930--31932
[]\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
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[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 31939--31941
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 31942--31944
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[460] [461] [462] [463] [464] [465]
Underfull \hbox (badness 10000) in paragraph at lines 32347--32351
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[466] [467] [468] [469] [470]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32703--32703
[] \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"),[]
[471] [472] [473] [474] [475] [476] [477]
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[] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[]
[478] [479] [480] [481] [482] [483]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33581--33581
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
[484] [485]
Underfull \hbox (badness 1158) in paragraph at lines 33685--33690
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal
and hex-adec-i-mal rep-re-sen-ta-tions
[486] [487]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 33870--33870
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
[488] [489] [490]
Underfull \hbox (badness 8151) in paragraph at lines 34130--34133
[]\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 .
[491] [492] [493] [494]
Underfull \hbox (badness 10000) in paragraph at lines 34345--34350
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10
gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by =
[495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506]
[507] [508] [509]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 35333--35333
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
[510] [511] [512]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 35585--35585
[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 35587--35587
[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
[513]
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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[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 35630--35636
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[514] [515]
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[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
[516] [517] [518] [519]
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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)[]
[520]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
[521] [522] [523] [524] [525] [526]
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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)[]
[527] [528] [529]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 36798--36798
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
[530] [531]
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[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 36889--36899
\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
Underfull \hbox (badness 1237) in paragraph at lines 36889--36899
\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 36889--36899
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n 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 36889--36899
\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
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[]\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 36935--36941
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 36935--36941
\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 36947--36954
[]\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 36947--36954
\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 36947--36954
\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
[532] [533] [534] [535]
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[]\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/
m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
[536]
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
[537] [538] [539] [540] [541] [542] [543] [544]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 37821--37821
[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
[545] [546] [547]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
[548]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
[549] [550] [551] [552] [553] [554] [555]
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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, ....[]
[556]
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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 38601--38608
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
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[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
[557] [558] [559] [560] [561]
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[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
[562] [563] [564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39130--39130
[]\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.
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[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
[565]
Underfull \hbox (badness 2293) in paragraph at lines 39198--39204
[]\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 39198--39204
\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 39217--39222
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
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\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
[566]
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\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 39307--39310
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[567] [568] [569]
Underfull \hbox (badness 10000) in paragraph at lines 39495--39499
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
Underfull \hbox (badness 1584) in paragraph at lines 39510--39513
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[570] [571]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 39642--39642
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
[572]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 39712--39712
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used
[573] [574] [575]
Underfull \hbox (badness 1082) in paragraph at lines 39856--39859
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577]
Underfull \hbox (badness 1038) in paragraph at lines 40047--40050
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[578] [579] [580] [581] [582] [583]
Underfull \hbox (badness 1442) in paragraph at lines 40408--40412
\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 =
[584] [585] [586]
Underfull \hbox (badness 4096) in paragraph at lines 40658--40661
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[587] [588]
Underfull \hbox (badness 7888) in paragraph at lines 40772--40776
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
length(bin) >
[589] [590]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40926--40926
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 40928--40928
[] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[]
[591]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40930--40930
[] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 40943--40945
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[592]
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[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[593] [594]
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[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[595]
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[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[596] [597] [598] [599] [600] [601]
Underfull \hbox (badness 10000) in paragraph at lines 41625--41632
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 41681--41690
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 41681--41690
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
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[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 41691--41699
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
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\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[602]
Underfull \hbox (badness 1337) in paragraph at lines 41757--41765
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[603]
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[][][]$\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-
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[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
[604] [605] [606]
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[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[607] [608]
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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:[]
[609] [610]
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[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
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[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
[611] [612] [613]
Underfull \hbox (badness 6542) in paragraph at lines 42555--42557
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
, and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[614] [615]
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
[616]
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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 e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 42742--42750
\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
[617]
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[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
and sup-press-ing the print-ing of er-ror mes-sages;
[618]
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[]\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 42834--42846
\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 ,
[619] [620] [621] [622]
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[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
[623] [624] [625] [626] [627] [628] [629]
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[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
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[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[]
[630]
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[][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[
][][]\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 ,
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[][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex
ists[][][]\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 ,
[631] [632]
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[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
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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
[633] [634] [635]
Underfull \hbox (badness 3668) in paragraph at lines 44072--44074
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[636] [637]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 44178--44178
[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[638]
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[]\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 ...[]
[639] [640]
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[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
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\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
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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 , namely a m
a-trix whose rows each
[641] [642]
Underfull \hbox (badness 2818) in paragraph at lines 44508--44514
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
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[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[643] [644]
Underfull \hbox (badness 1622) in paragraph at lines 44637--44639
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[645] [646] [647] [648] [649]
Underfull \hbox (badness 2846) in paragraph at lines 45000--45004
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[650]
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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-dard
' reg-exps, in-clud-ing el-e-ments named
[651]) (./compiler-pkg.tex [652]
Chapter 2.
[653]
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 be us
ed 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 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[654] [655] [656]) (./datasets-pkg.tex
Chapter 3.
[657] [658] [659] [660] [661]
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[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[662]
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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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[664] [665] [666] [667]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[668] [669]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 835--838
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[670] [671]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\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.
[672] [673]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[674] [675] [676] [677] [678]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[679] [680]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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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-tained from the a
bove
[681] [682] [683]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[684]
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[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
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[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[685] [686]
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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]]))))[]
[687] [688] [689] [690]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2152--2155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[691] [692] [693]
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[694] [695] [696] [697] [698]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[699]
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[700]
Underfull \vbox (badness 2376) has occurred while \output is active [701]
[702]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[703] [704]
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[705]
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[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[706] [707] [708] [709] [710] [711] [712]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[713] [714]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[715]
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[716]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[717]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
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[]\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 /
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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729]
[730] [731]) (./grDevices-pkg.tex [732]
Chapter 4.
[733] [734] [735] [736]
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[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
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[]\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/ptm/m/n/1
0 in
[737] [738]
Underfull \hbox (badness 10000) in paragraph at lines 379--387
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[739] [740]
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
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[]\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
[751] [752] [753]
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[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
Underfull \hbox (badness 1173) in paragraph at lines 1399--1402
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[754] [755] [756] [757] [758] [759] [760] [761]
Underfull \hbox (badness 1565) in paragraph at lines 1887--1892
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
pro-duce and print a postscript copy. This will not
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\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
[762]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
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[]\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-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[763] [764]
Underfull \hbox (badness 10000) in paragraph at lines 2123--2125
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[765] [766]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
[767] [768]
Underfull \hbox (badness 2326) in paragraph at lines 2419--2429
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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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
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[769] [770]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2522--2522
[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
Underfull \vbox (badness 10000) has occurred while \output is active [771]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2638--2638
[]\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 2639--2639
[]\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[]
[772] [773] [774] [775] [776]
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Underfull \vbox (badness 10000) has occurred while \output is active [777]
[778] [779] [780] [781]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3243--3243
[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[782]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3327--3327
[]\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 3328--3328
[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[783] [784]
Underfull \hbox (badness 10000) in paragraph at lines 3484--3489
[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
Underfull \hbox (badness 1264) in paragraph at lines 3484--3489
\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[785] [786]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3558--3558
[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[]
[787]
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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)[]
[788]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
[789]
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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 ,
[790]
Underfull \hbox (badness 2189) in paragraph at lines 3815--3820
[]\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we
ll for shad-ing points or lines in up to five groups,
Underfull \hbox (badness 10000) in paragraph at lines 3853--3857
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[791]
Underfull \vbox (badness 10000) has occurred while \output is active [792]
Underfull \hbox (badness 5260) in paragraph at lines 3983--3986
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[793] [794] [795] [796] [797]
Underfull \hbox (badness 5939) in paragraph at lines 4315--4320
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[798] [799] [800] [801] [802] [803]
Underfull \hbox (badness 10000) in paragraph at lines 4719--4724
[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
/ devnet / actionscript /
Underfull \hbox (badness 3612) in paragraph at lines 4719--4724
\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[804] [805]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4834--4834
[] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[]
[806] [807]
Underfull \hbox (badness 1348) in paragraph at lines 5039--5042
[]\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
[808]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5063--5063
[]\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 5104--5110
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[809]
Underfull \hbox (badness 1112) in paragraph at lines 5137--5141
[]\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"
[810]
Underfull \hbox (badness 1755) in paragraph at lines 5279--5281
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East
Asian lan-guages -- see
[811] [812] [813]
Underfull \hbox (badness 7344) in paragraph at lines 5459--5461
[]\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 5470--5474
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[814] [815]
Underfull \hbox (badness 1552) in paragraph at lines 5596--5605
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5596--5605
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[816]
Underfull \hbox (badness 10000) in paragraph at lines 5664--5671
[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[817] [818]
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[]\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[]
[819]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
[820] [821]
Underfull \hbox (badness 10000) in paragraph at lines 5963--5965
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
for on-screen de-vices and to
[822] [823] [824] [825] [826]
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[]\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 6344--6347
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[827] [828] [829] [830] [831] [832]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6679--6679
[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
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[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
[833] [834] [835] [836]
Underfull \hbox (badness 10000) in paragraph at lines 6949--6954
[]\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 y
pos\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 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[837]
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[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
[838]
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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 :
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7105--7105
[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
[839]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[840]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK
lan-guages and
[841]
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[842]
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[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[843]
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
[844] [845]
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\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 /
[846] [847]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[848] [849] [850]) (./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 =
[851] [852] [853]
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[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[854] [855] [856] [857]
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[] \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
[858] [859]
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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[]
[860]
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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
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[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[861] [862]
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
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[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
[863] [864] [865]
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[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/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-able.
Overfull \hbox (106.98032pt too wide) in paragraph at lines 981--981
[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[]
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[]\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 985--985
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
[866] [867] [868] [869]
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[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
[870] [871] [872]
Underfull \hbox (badness 1024) in paragraph at lines 1431--1439
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[873] [874]
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[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
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[]\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 1543--1543
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
[875] [876] [877] [878] [879]
Underfull \hbox (badness 10000) in paragraph at lines 1846--1852
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10
contourplot[][][] \T1/ptm/m/n/10 (and
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1878--1878
[]\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 = "")[]
[880] [881]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[882] [883]
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[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, 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))[]
[884] [885]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2296--2296
[]\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 = "",[]
[886]
Underfull \hbox (badness 1430) in paragraph at lines 2328--2330
[]\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
[887]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2409--2409
[] \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
[888]
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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[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
[889]
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[]\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[]
[890] [891] [892]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2750--2750
[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[893]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2787--2787
[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[894] [895]
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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
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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 :[]
[896]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[897] [898] [899]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3226--3226
[]\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 3231--3231
[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[900] [901]
Underfull \hbox (badness 10000) in paragraph at lines 3373--3378
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
raster im-ages are used when the
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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")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[902] [903] [904]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3559--3559
[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3578--3578
[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
[905]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3582--3582
[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[906] [907]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3759--3759
[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3760--3760
[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
[908]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3799--3799
[] \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 [909]
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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")[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3859--3859
[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3861--3861
[]\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 3869--3869
[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
[910]
Underfull \hbox (badness 10000) in paragraph at lines 3932--3936
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[911] [912]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4044--4044
[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[913] [914]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4198--4198
[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
[915]
Underfull \hbox (badness 3930) in paragraph at lines 4277--4279
[]\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
[916] [917] [918] [919] [920]
Underfull \hbox (badness 1286) in paragraph at lines 4588--4591
\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 4596--4601
[]\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
[921] [922]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4693--4693
[]\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))[]
[923]
Underfull \hbox (badness 1264) in paragraph at lines 4889--4902
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[924] [925]
Underfull \hbox (badness 10000) in paragraph at lines 5026--5032
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[926] [927]
Underfull \hbox (badness 10000) in paragraph at lines 5157--5160
[928 </usr/src/RPM/BUILD/R-4.0.2/library/graphics/help/figures/mai.pdf>]
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[929 </usr/src/RPM/BUILD/R-4.0.2/library/graphics/help/figures/oma.pdf>]
[930]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[931]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5464--5464
[]\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 5465--5465
[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
Underfull \vbox (badness 10000) has occurred while \output is active [932]
[933] [934] [935] [936] [937]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5830--5830
[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5831--5831
[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
[938]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again>
\relax
l.5890 \aliasA{plot}{plot.default}{plot}
[939] [940] [941] [942] [943]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6222--6222
[]\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v
ector ~ factor[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6228--6228
[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[944] [945] [946] [947] [948] [949]
Underfull \hbox (badness 10000) in paragraph at lines 6658--6660
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[950] [951]
Underfull \hbox (badness 1028) in paragraph at lines 6752--6754
[]\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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[][]
[952 </usr/src/RPM/BUILD/R-4.0.2/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,[]
[953]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6920--6920
[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
Underfull \vbox (badness 10000) has occurred while \output is active [954]
[955]
Underfull \hbox (badness 10000) in paragraph at lines 7042--7044
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7069--7069
[] \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)))))[]
[956]
Underfull \hbox (badness 2600) in paragraph at lines 7135--7137
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[957] [958] [959] [960]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7367--7367
[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[961] [962] [963] [964] [965] [966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7754--7754
[]\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):[]
[967]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7770--7770
[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[968] [969] [970] [971] [972]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8119--8119
[]\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,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8126--8126
[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[973] [974] [975]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8297--8297
[]\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, ...)[]
[976] [977]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
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[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[978]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[979]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8521--8521
[]\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),[]
[980] [981]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8673--8673
[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
[982] [983]
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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...")[]
[984]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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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 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[985]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again>
\relax
l.8968 \HeaderA{units}{Graphical Units}{units}
[986]
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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
[987] [988]
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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)[]
[989]) (./grid-pkg.tex [990]
Chapter 6.
[991] [992] [993] [994] [995] [996] [997] [998]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1009] [1010] [1011] [1012]
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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
[1013] [1014] [1015] [1016] [1017] [1018]
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
[1019] [1020] [1021]
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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")[]
[1022]
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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 ,
[1023]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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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
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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
[1027] [1028] [1029]
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1030]
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
[1031] [1032]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
[1033] [1034] [1035] [1036]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
[1037] [1038] [1039] [1040] [1041]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
[1042]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
"bottom")))[]
[1043]
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1044] [1045]
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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,[]
[1046] [1047] [1048]
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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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[1061]
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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
[1062]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1063] [1064] [1065]
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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 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
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[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
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\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1086] [1087] [1088] [1089] [1090]
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
[1091]
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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
[1092]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1093] [1094]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
do-ing some-thing like \T1/pcr/m/n/10 depth
[1095]
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[1097] [1098]
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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"))))[]
[1099]) (./methods-pkg.tex [1100]
Chapter 7.
[1101] [1102]
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\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1103] [1104] [1105]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1106] [1107]
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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[]
[1108]
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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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[1122] [1123] [1124]
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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[]
[1125] [1126]
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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 c
an be an ob-ject of class
[1127] [1128] [1129]
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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 =
[1130] [1131]
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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
[1132] [1133] [1134]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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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
[1135]
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
[1136] [1137] [1138]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
[1139] [1140] [1141] [1142] [1143] [1144] [1145]
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[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
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\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1146] [1147]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1148]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these
classes takes spe-cial ar-gu-ments
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[]
[1149] [1150]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
=
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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1151]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
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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
[1152] [1153] [1154]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1155] [1156] [1157]
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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,[]
[1158]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
[1159] [1160] [1161]
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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 ,
[1162] [1163] [1164]
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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
[1165] [1166] [1167] [1168]
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
[1169]
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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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[1171]
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[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1172] [1173]
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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
[1174] [1175] [1176]
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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/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1183] [1184]
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
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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
[1185]
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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
[1186] [1187]
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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
[1188]
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[1190] [1191]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again>
\relax
l.6973 \aliasA{S4}{S3Part}{S4}
[1192]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
[1193] [1194]
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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")[]
[1195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again>
\relax
l.7229 \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.7231 \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.7232 \aliasA{Math}{S4groupGeneric}{Math}
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th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again>
\relax
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again>
\relax
l.7235 \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
[1196]
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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/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1197] [1198]
Underfull \hbox (badness 1694) in paragraph at lines 7472--7474
[]\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 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1199] [1200]
Underfull \hbox (badness 1019) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
\T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1212]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622
[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
[1213]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697
[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
[1214] [1215] [1216] [1217]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959
[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
[1218] [1219] [1220]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167
[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
[1221] [1222] [1223]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429
[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
[1224] [1225] [1226] [1227]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737
[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
[1228]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847
[]\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 9858--9858
[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
[1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238]
Underfull \hbox (badness 10000) in paragraph at lines 10556--10558
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\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 10564--10568
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1239] [1240] [1241]) (./parallel-pkg.tex [1242]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1243]
Underfull \hbox (badness 4242) in paragraph at lines 96--98
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1244] [1245]
Underfull \hbox (badness 1024) in paragraph at lines 213--216
[]\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
[1246] [1247] [1248]
Underfull \hbox (badness 10000) in paragraph at lines 449--451
[]\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
[1249] [1250] [1251] [1252] [1253]
Underfull \hbox (badness 1917) in paragraph at lines 755--764
[]\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 755--764
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1254]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 848--848
[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
[1255] [1256] [1257]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1039--1039
[]\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 1043--1043
[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1258] [1259]
Underfull \hbox (badness 5388) in paragraph at lines 1158--1163
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 1182--1190
[]\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
[1260]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1219--1219
[]\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)[]
[1261]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1335--1335
[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
[1262]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1349--1349
[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
Underfull \hbox (badness 1577) in paragraph at lines 1378--1381
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1263]
Underfull \hbox (badness 3375) in paragraph at lines 1425--1427
[]\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
[1264] [1265]) (./splines-pkg.tex [1266]
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
[1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1275]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
-1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1276] [1277]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
[1278] [1279] [1280]) (./stats-pkg.tex
Chapter 10.
[1281]
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 o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
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[]
[1282] [1283] [1284] [1285] [1286]
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[]
[1287]
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)
[1288] [1289] [1290] [1291] [1292] [1293]
Underfull \hbox (badness 1024) in paragraph at lines 879--881
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303]
Underfull \hbox (badness 10000) in paragraph at lines 1541--1545
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1541--1545
\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1541--1545
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1304]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1617--1617
[] \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 1620--1620
[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
[1305] [1306]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767
[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
[1307]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1779--1779
[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$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 :[
]
[1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318]
[1319] [1320]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2770--2770
[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
[1321] [1322] [1323] [1324]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3010--3010
[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
[1325] [1326] [1327]
Underfull \hbox (badness 10000) in paragraph at lines 3220--3222
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1328]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3269--3269
[]\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 3270--3270
[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
[1329] [1330] [1331] [1332] [1333] [1334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3661--3661
[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
[1335] [1336] [1337] [1338]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3940--3940
[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
[1339] [1340] [1341] [1342] [1343]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4229--4229
[]\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 4230--4230
[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
[1344] [1345] [1346]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4469--4469
[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
[1347] [1348] [1349]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4644--4644
[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
[1350]
Underfull \hbox (badness 3989) in paragraph at lines 4738--4745
[]\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 =
[1351] [1352] [1353] [1354] [1355] [1356]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5123--5123
[]\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 5125--5125
[]\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))[]
[1357] [1358] [1359]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5346--5346
[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5364--5364
[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
Underfull \hbox (badness 2680) in paragraph at lines 5391--5393
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is
given by
[1360] [1361] [1362]
Underfull \hbox (badness 1436) in paragraph at lines 5574--5579
[]\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 5574--5579
\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 5574--5579
\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 ,
[1363] [1364] [1365]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5777--5777
[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
[1366] [1367] [1368]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5944--5944
[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
[1369] [1370] [1371]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6129--6129
[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
[1372]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6237--6237
[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
[1373]
Underfull \hbox (badness 10000) in paragraph at lines 6304--6309
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1374] [1375] [1376] [1377]
Underfull \hbox (badness 5954) in paragraph at lines 6500--6502
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1378]
Underfull \hbox (badness 2503) in paragraph at lines 6582--6585
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6586--6588
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6589--6594
\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,
Underfull \hbox (badness 7238) in paragraph at lines 6625--6628
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1379]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6660--6660
[]\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):[]
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[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
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[1381] [1382] [1383]
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[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
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Underfull \hbox (badness 10000) in paragraph at lines 7333--7337
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1390]
Underfull \hbox (badness 6493) in paragraph at lines 7432--7435
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1391] [1392]
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[]\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 =
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Underfull \hbox (badness 10000) in paragraph at lines 7981--7986
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
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Underfull \hbox (badness 1210) in paragraph at lines 8336--8338
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
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[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
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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))[]
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[]\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
.90) # ~= 7e-9[]
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[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
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[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
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Underfull \hbox (badness 7291) in paragraph at lines 9592--9594
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
homogeneity of
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Underfull \hbox (badness 6944) in paragraph at lines 10070--10076
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1430] [1431] [1432] [1433]
Underfull \hbox (badness 3758) in paragraph at lines 10284--10287
[]\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
[1434] [1435] [1436]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10528--10528
[] \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
[1437]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1438]
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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 \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
Underfull \hbox (badness 10000) in paragraph at lines 10698--10701
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
fitted.values \T1/ptm/m/n/10 and
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Underfull \hbox (badness 2142) in paragraph at lines 10915--10918
[]\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 ^^@
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Underfull \hbox (badness 1708) in paragraph at lines 10996--11000
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
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[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
[1444]
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\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
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Underfull \hbox (badness 2635) in paragraph at lines 11209--11212
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
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Underfull \hbox (badness 1694) in paragraph at lines 11392--11395
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
[1449] [1450]
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
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[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
[1451]
Underfull \hbox (badness 10000) in paragraph at lines 11539--11543
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1452] [1453] [1454] [1455] [1456]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11861--11861
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.11876 \aliasA{hat}{influence.measures}{hat}
[1457]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11936--11936
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
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[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
[1458]
Underfull \hbox (badness 1062) in paragraph at lines 12001--12006
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12018--12020
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1459] [1460] [1461] [1462]
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[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
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[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
[1463]
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[] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
= "tobacco",[]
[1464] [1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 12616--12618
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
[1468]
Underfull \hbox (badness 4739) in paragraph at lines 12639--12641
[]\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
[1469]
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[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
/ / bugs . r-[]project . org / bugzilla3 /
[1470] [1471] [1472]
Underfull \hbox (badness 6910) in paragraph at lines 12946--12948
[]\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
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[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
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\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 13659--13659
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
[1484]
Underfull \hbox (badness 4518) in paragraph at lines 13703--13708
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486]
Underfull \hbox (badness 10000) in paragraph at lines 13902--13906
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
,
[1487] [1488] [1489] [1490] [1491]
Underfull \hbox (badness 1163) in paragraph at lines 14236--14244
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1492] [1493]
Underfull \hbox (badness 4518) in paragraph at lines 14356--14361
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1494] [1495] [1496]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14544--14544
[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1497] [1498] [1499] [1500] [1501]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14888--14888
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
[1502] [1503]
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[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
[1504] [1505] [1506] [1507] [1508] [1509]
Underfull \hbox (badness 2726) in paragraph at lines 15388--15391
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1510]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15482--15482
[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
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[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
[1521] [1522]
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\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
[1523]
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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 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
sup-ply vari-ables with the same names as would
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\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1524]
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[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b
= contr.poly))[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 16955--16955
[]\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[]
[1534] [1535] [1536]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17187--17187
[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
[1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 17948--17948
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
[1549] [1550] [1551]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18111--18111
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
[1552]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
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Underfull \hbox (badness 1248) in paragraph at lines 18703--18706
[]\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
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[]\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
[1561]
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\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
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[]\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
[1562] [1563]
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[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
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[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
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[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
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[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
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[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
[1565]
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19010--19021
\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
[1566]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19073--19073
[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
[1567] [1568] [1569]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19299--19299
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
[1570] [1571]
Underfull \hbox (badness 1337) in paragraph at lines 19410--19413
[]\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
[1572] [1573] [1574] [1575] [1576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19729--19729
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
[1577] [1578]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19817--19817
[] \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 19819--19819
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19821--19821
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1579]
Underfull \hbox (badness 10000) in paragraph at lines 19867--19873
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 3049) in paragraph at lines 19908--19912
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1580] [1581] [1582] [1583]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20161--20161
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
Underfull \hbox (badness 1194) in paragraph at lines 20171--20174
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1584]
Underfull \hbox (badness 1107) in paragraph at lines 20229--20231
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1585]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20284--20284
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20291--20291
[]\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)[]
[1587]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20385--20385
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
[1588] [1589]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20514--20514
[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1590]
Underfull \hbox (badness 7740) in paragraph at lines 20577--20579
[]\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
[1591]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20625--20625
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
[1592]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20717--20717
[] \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 20722--20722
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
[1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603]
[1604] [1605]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21577--21577
[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
equal typically[]
[1606]
Underfull \hbox (badness 6859) in paragraph at lines 21644--21651
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21655--21661
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617]
[1618]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22401--22401
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
[1619] [1620] [1621] [1622] [1623]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22685--22685
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22686--22686
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
[1624] [1625] [1626] [1627] [1628]
Underfull \hbox (badness 1337) in paragraph at lines 23012--23018
[]\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
[1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23579--23579
[] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[]
[1637] [1638]
Underfull \hbox (badness 1028) in paragraph at lines 23720--23723
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1639] [1640]
Underfull \hbox (badness 10000) in paragraph at lines 23830--23833
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1641]
Underfull \hbox (badness 7944) in paragraph at lines 23885--23887
[]\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,levels =
[1642]
Underfull \hbox (badness 7944) in paragraph at lines 23947--23949
[]\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,levels =
[1643] [1644]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24049--24049
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1645] [1646] [1647]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24269--24269
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1648]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24373--24373
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
[1649]
Underfull \hbox (badness 1033) in paragraph at lines 24416--24422
\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 24437--24440
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1650]
Underfull \hbox (badness 2134) in paragraph at lines 24506--24510
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24519--24519
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
[1651]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24548--24548
[]\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 24560--24560
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
[1652] [1653] [1654] [1655] [1656] [1657] [1658]
Underfull \hbox (badness 6268) in paragraph at lines 25015--25020
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/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 ,
[1659]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 25043--25043
[] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[]
[1660] [1661] [1662]
Underfull \hbox (badness 1867) in paragraph at lines 25220--25222
[]\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 25235--25239
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback =
use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25235--25239
\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 25271--25271
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
[1663] [1664] [1665]
Underfull \hbox (badness 2495) in paragraph at lines 25461--25470
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1666]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25543--25543
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
[1667]
Underfull \hbox (badness 1412) in paragraph at lines 25550--25552
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1668]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25637--25637
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25662--25662
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25665--25665
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
[1669] [1670] [1671]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 25889--25889
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 25893--25899
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1672]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25939--25939
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25960--25960
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1673]
Underfull \hbox (badness 1019) in paragraph at lines 26022--26027
\T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow
\T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value
[1674] [1675]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26152--26152
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1676] [1677] [1678] [1679] [1680] [1681]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26531--26531
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1682] [1683]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26712--26712
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
[1684]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26718--26718
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean) f
or when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26727--26727
[]\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 26728--26728
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
[1685]
Underfull \hbox (badness 2922) in paragraph at lines 26797--26802
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26834--26834
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
[1686]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26837--26837
[] \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 26846--26846
[] \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 26847--26847
[] \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 26851--26851
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1687]
Underfull \hbox (badness 3240) in paragraph at lines 26905--26908
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26926--26926
[] \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 26929--26929
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1688]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27012--27012
[] \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 27016--27016
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
[1689]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 27026--27026
[] \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 27031--27031
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
Underfull \hbox (badness 2922) in paragraph at lines 27067--27073
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1690]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27089--27089
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27105--27105
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
[1691] [1692]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 27219--27219
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1693]
Underfull \hbox (badness 2922) in paragraph at lines 27281--27286
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27319--27319
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
[1694]
Underfull \hbox (badness 2922) in paragraph at lines 27368--27373
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1695]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27399--27399
[]\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 27433--27438
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1696]
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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[]
[1697]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
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[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1698]
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[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1699]
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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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[1711] [1712] [1713]
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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
[1714] [1715] [1716]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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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
[1719]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1720]
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1721] [1722]
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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)
[1723] [1724]
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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
[1725] [1726] [1727] [1728]
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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",[]
[1729]
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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
[1730]
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1731]
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1732] [1733]
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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 giv
en 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)[]
[1743] [1744] [1745] [1746] [1747]
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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)[]
[1748] [1749]
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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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[1751] [1752]
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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-
e-sis, must be one of
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[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i
-tive nu-meric tol-er-ance, used in
[1762] [1763] [1764]
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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)[]
[1765] [1766]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
= getOption("ts.eps"), ...)[]
[1767]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
[1768]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1769]
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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 "")[]
[1770]) (./stats4-pkg.tex
Chapter 11.
[1771] [1772] [1773]
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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[]
[1775] [1776] [1777] [1778]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}
[1779] [1780] [1781])
(./tcltk-pkg.tex [1782]
Chapter 12.
[1783] [1784] [1785] [1786]
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
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-ing
any Tk or Tcl com-mand by sim-ply run-ning
[1791] [1792] [1793] [1794] [1795] [1796]
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[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
[1797] [1798] [1799] [1800] [1801]
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1802]) (./tools-pkg.tex
Chapter 13.
[1803]
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
[1804]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
which will be eval-u-ated via
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1805]
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
[1806]
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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/1
0 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/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1807]
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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-gine
to use. Over-rides any
[1808] [1809]
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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")[]
[1817] [1818] [1819]
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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 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:
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\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1820]
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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/p
tm/m/n/10 and
[1821]
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[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
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[] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[]
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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","Enhances")\T1/ptm/
m/n/10 .
[1829] [1830] [1831]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
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l.1911 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
[1832] [1833] [1834]
[1835]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
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[]\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[]
[1836]
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[] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[]
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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
[1837]
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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
[1838]
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[]\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[]
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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","Enhances")\T1/ptm/
m/n/10 .
[1839]
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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/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[]
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[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
= TRUE)[]
[1840] [1841] [1842] [1843]
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[]
[1844]
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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
[1845] [1846] [1847] [1848] [1849]
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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-to
r 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"))[]
[1855] [1856] [1857] [1858]
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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
,
Underfull \hbox (badness 2932) in paragraph at lines 3866--3872
[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1861] [1862]
Underfull \hbox (badness 7832) in paragraph at lines 3988--3991
[]\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1863]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4064--4064
[] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[]
[1864]
Underfull \hbox (badness 1137) in paragraph at lines 4090--4092
[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
sys-tem, as from
[1865] [1866] [1867]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4275--4275
[] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[]
[1868] [1869]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4437--4437
[]\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright,
bugs)
Underfull \hbox (badness 10000) in paragraph at lines 4448--4451
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
[1870]
Underfull \hbox (badness 6859) in paragraph at lines 4464--4469
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 4472--4478
[]\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
[1871] [1872] [1873] [1874]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4730--4730
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4731--4731
[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[]
Underfull \hbox (badness 3240) in paragraph at lines 4743--4746
[]\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 4747--4757
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4782--4788
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4782--4788
\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 ',
[1875]
Underfull \hbox (badness 1571) in paragraph at lines 4810--4814
[]\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 4836--4841
\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
[1876] [1877] [1878]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1879] [1880] [1881] [1882]
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[]
[1883]
Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383
\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1884]
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
[1885]
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"))[]
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[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1886] [1887]
Underfull \hbox (badness 1946) in paragraph at lines 626--630
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1888]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 676--676
[]\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 683--683
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 684--684
[]\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 685--685
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Underfull \hbox (badness 10000) in paragraph at lines 719--725
[]\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 719--725
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1889] [1890]
Underfull \hbox (badness 4505) in paragraph at lines 855--861
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1891] [1892] [1893]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1029--1029
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1894]
Underfull \hbox (badness 1748) in paragraph at lines 1094--1102
[]\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-
Underfull \hbox (badness 1661) in paragraph at lines 1094--1102
\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 1094--1102
\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 1106--1108
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1895]
Underfull \hbox (badness 10000) in paragraph at lines 1214--1217
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1896]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1297--1297
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1799--1799
[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1834--1834
[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[1905] [1906]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1980--1980
[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[1907] [1908]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2132--2132
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1909]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2184--2184
[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[1910] [1911] [1912]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2353--2353
[] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2376--2376
[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[1913] [1914]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2496--2496
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1915]
Underfull \hbox (badness 1082) in paragraph at lines 2570--2574
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2575 ... the Clipboard in MS Windows}{clipboard}
Underfull \hbox (badness 1163) in paragraph at lines 2606--2608
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1916] [1917]
Underfull \hbox (badness 10000) in paragraph at lines 2694--2696
[]\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
[1918] [1919] [1920]
Underfull \hbox (badness 10000) in paragraph at lines 2911--2913
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1921] [1922] [1923] [1924]
Underfull \hbox (badness 1762) in paragraph at lines 3205--3208
[]\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 =
[1925]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3298--3298
[]\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 '[]
[1926]
Underfull \hbox (badness 2452) in paragraph at lines 3374--3377
[]\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
[1927] [1928] [1929] [1930] [1931] [1932]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3783--3783
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[1933] [1934]
Underfull \hbox (badness 10000) in paragraph at lines 3867--3871
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is
op-tional on Win-dows: use
Underfull \hbox (badness 1072) in paragraph at lines 3924--3932
[]\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
[1935]
Underfull \hbox (badness 1231) in paragraph at lines 4001--4013
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 4015--4020
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method =
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 4015--4020
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
of
Underfull \hbox (badness 1331) in paragraph at lines 4015--4020
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
brack-ets are op-tional. See
[1936] [1937]
Underfull \hbox (badness 4660) in paragraph at lines 4135--4138
\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
Underfull \hbox (badness 10000) in paragraph at lines 4159--4161
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1938] [1939] [1940]
Underfull \hbox (badness 1565) in paragraph at lines 4344--4348
[]\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
[1941]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4427--4427
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[1942]
Underfull \hbox (badness 1931) in paragraph at lines 4462--4469
[]\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)
[1943] [1944] [1945] [1946] [1947]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4786--4786
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[1948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again>
\relax
l.4857 ...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.4857 ...mat Unordered and Ordered Lists}{format}
[1949] [1950] [1951]
[1952] [1953] [1954] [1955] [1956]
Underfull \hbox (badness 1622) in paragraph at lines 5376--5380
[]\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
[1957] [1958] [1959] [1960] [1961]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 5698--5698
[]\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 5710--5710
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
[1962] [1963]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5843--5843
[] \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 5844--5844
[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
[1964] [1965] [1966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6054--6054
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[1967]
Underfull \hbox (badness 10000) in paragraph at lines 6138--6140
[]\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
[1968]
Underfull \hbox (badness 1502) in paragraph at lines 6187--6192
[]\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 6187--6192
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
[1969] [1970]
Underfull \hbox (badness 10000) in paragraph at lines 6360--6369
[]\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 6360--6369
\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
[1971]
Underfull \hbox (badness 2150) in paragraph at lines 6424--6427
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6440--6443
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search
database for sub-se-quent use by
[1972] [1973]
Underfull \hbox (badness 3118) in paragraph at lines 6562--6564
[]\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
[1974] [1975]
Underfull \hbox (badness 5091) in paragraph at lines 6736--6738
[]\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
[1976]
Underfull \hbox (badness 5331) in paragraph at lines 6752--6758
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6752--6758
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6752--6758
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6766--6773
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
Underfull \hbox (badness 1270) in paragraph at lines 6781--6791
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
[1977]
Underfull \hbox (badness 10000) in paragraph at lines 6824--6827
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be
Underfull \hbox (badness 10000) in paragraph at lines 6824--6827
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
Underfull \hbox (badness 1424) in paragraph at lines 6832--6835
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 6889--6893
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
[1978]
Underfull \hbox (badness 2376) in paragraph at lines 6903--6910
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 6903--6910
\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 6903--6910
\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 6911--6914
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1979]
Underfull \hbox (badness 1314) in paragraph at lines 6990--6997
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
Underfull \hbox (badness 10000) in paragraph at lines 7047--7052
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7070--7070
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
[1980]
Underfull \hbox (badness 5133) in paragraph at lines 7106--7110
[]\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 7120--7123
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1981]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7167--7167
[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
[1982] [1983]
Underfull \hbox (badness 4132) in paragraph at lines 7287--7289
[]\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
[1984] [1985] [1986]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7454--7454
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[1987] [1988]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7597--7597
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[1989]
Underfull \hbox (badness 10000) in paragraph at lines 7637--7639
[]\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
[1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 7825--7827
[]\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 7830--7832
[]\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
[1992] [1993] [1994] [1995]
Underfull \hbox (badness 1859) in paragraph at lines 8058--8061
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1996]
Underfull \hbox (badness 1655) in paragraph at lines 8152--8155
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8163--8163
[]\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 8171--8171
[]\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):[]
[1997]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8179--8179
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[1998]
Underfull \hbox (badness 1917) in paragraph at lines 8266--8268
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[1999] [2000] [2001] [2002]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8538--8538
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8539--8539
[] \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 8540--8540
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[2003]
Underfull \hbox (badness 10000) in paragraph at lines 8568--8570
[]\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 8582--8584
[]\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 8590--8595
[]\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,
[2004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8636--8636
[] \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 8637--8637
[] \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[]
[2005] [2006]
Underfull \hbox (badness 10000) in paragraph at lines 8766--8771
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8766--8771
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8766--8771
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8773--8776
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[2007]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8889--8889
[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8890--8890
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[2008] [2009] [2010]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9061--9061
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[2011]
Underfull \hbox (badness 1789) in paragraph at lines 9192--9194
[]\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
[2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020]
Underfull \hbox (badness 5203) in paragraph at lines 9765--9768
[]\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
[2021] [2022]
Underfull \hbox (badness 1394) in paragraph at lines 9991--9998
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
, try-ing to com-plete
[2023]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10015--10015
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[2024] [2025]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10176--10176
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[2026] [2027] [2028]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10357--10357
[]\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[]
[2029]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10443--10443
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10446--10446
[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10451--10451
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2030]
Underfull \hbox (badness 2027) in paragraph at lines 10523--10526
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[2031] [2032] [2033] [2034]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10795--10795
[]\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 10796--10796
[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
Underfull \hbox (badness 10000) in paragraph at lines 10803--10808
[]\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 10803--10808
\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 10803--10808
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2035] [2036] [2037]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11036--11036
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2038] [2039] [2040] [2041] [2042]
Underfull \hbox (badness 10000) in paragraph at lines 11297--11301
\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 11315--11315
[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11320--11320
[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,3899} :[]
[2043] [2044]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11453--11453
[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 11454--11454
[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
[2045] [2046]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11589--11589
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[2047]
Underfull \hbox (badness 1917) in paragraph at lines 11713--11716
[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
Underfull \hbox (badness 4328) in paragraph at lines 11713--11716
\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
[2048]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 11736--11736
[]\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 '[]
[2049]
Underfull \hbox (badness 10000) in paragraph at lines 11799--11801
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
[2050]
Underfull \hbox (badness 6725) in paragraph at lines 11849--11858
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
Underfull \hbox (badness 6428) in paragraph at lines 11849--11858
\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 11849--11858
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 11849--11858
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2051]
Underfull \hbox (badness 3646) in paragraph at lines 11975--11977
[][][]$\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 /
[2052]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12013--12013
[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
[2053] [2054] [2055]
Underfull \hbox (badness 10000) in paragraph at lines 12194--12198
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12225--12231
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2056] [2057]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12401--12401
[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
[2058]
Underfull \hbox (badness 1009) in paragraph at lines 12419--12431
[]\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 12459--12461
[]\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
[2059]
Underfull \hbox (badness 1043) in paragraph at lines 12502--12507
[]\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
[2060] [2061] [2062] [2063]
Underfull \hbox (badness 1888) in paragraph at lines 12795--12798
[]\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 12812--12815
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2064]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12853--12853
[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
[2065]
Underfull \hbox (badness 2158) in paragraph at lines 12908--12911
[]\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 12956--12956
[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
[2066] [2067] [2068]
Underfull \hbox (badness 2302) in paragraph at lines 13113--13115
[]\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
[2069]
Underfull \hbox (badness 3333) in paragraph at lines 13220--13222
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2070] [2071] [2072]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 13387--13387
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
Underfull \hbox (badness 2012) in paragraph at lines 13411--13416
[]\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 have
Underfull \hbox (badness 5970) in paragraph at lines 13420--13423
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13420--13423
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2073]
Underfull \hbox (badness 1442) in paragraph at lines 13447--13451
[]\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault,
de-ter-min-ing the \T1/pcr/m/n/10 nlines \T1/ptm/m/n/10 ar-gu-ment to
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13479--13479
[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2074]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 13510--13510
[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13517--13517
[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13519--13519
[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
[2075] [2076]
Underfull \hbox (badness 10000) in paragraph at lines 13687--13689
[]\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
[2077] [2078] [2079]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 13844--13851
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
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\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$"\T1/ptm/m/n/10 ) and
[2080] [2081]
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\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 14013--14029
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2082] [2083]
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[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2084] [2085] [2086]
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[] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[]
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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
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.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 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 14826--14831
\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 14826--14831
\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \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
[2093]
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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 av
ailable.packages(contriburl =
Underfull \hbox (badness 1509) in paragraph at lines 14862--14867
\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
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 14883--14888
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 14891--14894
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2094]
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[]\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt")
[2095] [2096] [2097]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2098]
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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:[]
[2099]
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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)))[]
[2100] [2101]
Underfull \hbox (badness 1297) in paragraph at lines 15383--15385
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2102]
Underfull \hbox (badness 4036) in paragraph at lines 15430--15432
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2103] [2104]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
[2105]
Underfull \hbox (badness 1715) in paragraph at lines 15619--15622
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15664--15666
[]\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 =
[2106] [2107] [2108]) [2109] [2110] (./KernSmooth-pkg.tex
Chapter 15.
[2111]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2112] [2113] [2114] [2115] [2116]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2117] [2118] [2119] [2120]) (./MASS-pkg.tex
Chapter 16.
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774
[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
[2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142]
[2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
[2154]
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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"),[]
[2155] [2156] [2157] [2158]
Underfull \hbox (badness 6559) in paragraph at lines 2698--2701
[]\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
[2159] [2160] [2161]
Underfull \hbox (badness 10000) in paragraph at lines 2868--2873
\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2868--2873
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\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 ,
[2162] [2163]
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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
[2164] [2165] [2166]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3231--3231
[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
[2167]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
[2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178]
[2179]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2180] [2181] [2182] [2183] [2184] [2185] [2186]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4645--4645
[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
[2187] [2188] [2189]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
[2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200]
[2201] [2202] [2203]
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
[2204]
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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")
[2205] [2206]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again>
\relax
l.6123 ...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.6123 ...sical N, P, K Factorial Experiment}{npk}
[2207]
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[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space.
That is
[2208] [2209] [2210] [2211]
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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)))[]
[2213]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
[2214] [2215] [2216] [2217] [2218] [2219]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7070--7070
[]\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"))[]
[2220]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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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 ) =
[2221]
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
[2222] [2223]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2224] [2225]
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
[2226]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
[2227] [2228] [2229] [2230] [2231] [2232]
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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
[2233] [2234]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8096--8096
[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
Underfull \hbox (badness 1590) in paragraph at lines 8120--8124
[]\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
[2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245]
[2246] [2247] [2248] [2249] [2250] [2251] [2252] [2253] [2254]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9499--9499
[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2255]
Underfull \hbox (badness 2035) in paragraph at lines 9611--9613
[]\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 ,
Underfull \hbox (badness 1158) in paragraph at lines 9626--9629
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
"Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2256]
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[]\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 9710--9710
[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9713--9713
[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
[2257] [2258] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267]
[2268] [2269]) (./Matrix-pkg.tex [2270]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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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
[2271]
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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
[2272]
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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
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\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2273]
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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 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2274] [2275]
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[]\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE)
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal
mean-ing as in
[2276]
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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
Underfull \hbox (badness 4621) in paragraph at lines 512--516
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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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)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546
[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[]
[2277] [2278]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many* (k x k) matrices:[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<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 662--662
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k)
matrix of class \code{"\linkS4class{dgCMatrix}"}.[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675
[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676
[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681
[]\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[]
[2279]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2280] [2281] [2282]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947
[]\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[]
[2283] [2284]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again>
\relax
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
[2285pdfTeX warning (ext4):
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.1163 ## S4 method for signature 'dsparseMatrix'
]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2286]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266
[]\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[]
[2287]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1361--1361
[]\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
0, ...)
Underfull \hbox (badness 2277) in paragraph at lines 1389--1392
[]\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
[2288]
Underfull \hbox (badness 1609) in paragraph at lines 1436--1440
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2289]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1463--1463
[]\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1477--1477
[]\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[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1485--1485
[]\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[]
[2290]
Underfull \hbox (badness 10000) in paragraph at lines 1532--1539
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1532--1539
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
Underfull \hbox (badness 1783) in paragraph at lines 1567--1571
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1583--1589
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2291]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again>
\relax
l.1624 ... 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.1624 ... 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.1625 \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.1646 \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.1657 \aliasA{rowSums}{colSums}{rowSums}
[2292]
Underfull \hbox (badness 2922) in paragraph at lines 1711--1715
[]\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 1711--1715
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1722--1725
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2293] [2294]
Underfull \hbox (badness 3547) in paragraph at lines 1876--1879
[]\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
[2295] [2296] [2297] [2298] [2299]
Underfull \hbox (badness 1484) in paragraph at lines 2238--2240
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2300]
Underfull \hbox (badness 7379) in paragraph at lines 2334--2336
[]\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
[2301] [2302] [2303]
Underfull \hbox (badness 4846) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2368) in paragraph at lines 2615--2619
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2622--2625
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2304]
Underfull \hbox (badness 2689) in paragraph at lines 2678--2680
[]\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 2682--2687
[]\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 2682--2687
[][]\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
[2305]
Underfull \hbox (badness 1097) in paragraph at lines 2705--2708
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2718--2723
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2306]
Underfull \hbox (badness 3646) in paragraph at lines 2957--2960
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 2989--2991
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 2992--2996
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 3001--3007
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2307]
Underfull \hbox (badness 10000) in paragraph at lines 3008--3012
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3018--3022
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2308] [2309]
Underfull \hbox (badness 10000) in paragraph at lines 3202--3204
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3249--3251
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2310]
Underfull \hbox (badness 2469) in paragraph at lines 3369--3372
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
, via
[2311] [2312]
Underfull \hbox (badness 10000) in paragraph at lines 3534--3538
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3534--3538
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2313]
Underfull \hbox (badness 2285) in paragraph at lines 3584--3587
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2314] [2315]
Underfull \hbox (badness 10000) in paragraph at lines 3731--3736
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3731--3736
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3743--3746
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 :
if \T1/pcr/m/n/10 uplo ==
[2316]
Underfull \hbox (badness 10000) in paragraph at lines 3819--3821
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2317] [2318] [2319]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4029--4029
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 4097--4101
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
[2320]
Underfull \hbox (badness 10000) in paragraph at lines 4106--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4106--4109
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4111--4115
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
: the
[2321] [2322]
Underfull \hbox (badness 3158) in paragraph at lines 4294--4298
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2323] [2324] [2325] [2326]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4533--4533
[] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[]
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[] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4540--4540
[]\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 4543--4543
[]\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():[]
[2327] [2328] [2329] [2330]
Underfull \hbox (badness 10000) in paragraph at lines 4855--4860
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2331]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4936--4936
[]\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 4938--4938
[] \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 4942--4942
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2332]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4949--4949
[] \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 '[]
[2333] [2334]
Underfull \hbox (badness 4120) in paragraph at lines 5093--5096
[]\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 (15.18042pt too wide) in paragraph at lines 5130--5130
[]\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 5136--5136
[] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,
border.col=NA)[]
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[] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[]
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[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5142--5142
[]\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[]
[2335]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5149--5149
[]\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[]
[2336]
Underfull \hbox (badness 1817) in paragraph at lines 5241--5250
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
the
Underfull \hbox (badness 10000) in paragraph at lines 5283--5285
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5285--5288
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2337]
Underfull \hbox (badness 4765) in paragraph at lines 5316--5319
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2338]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5376--5376
[] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[]
[2339] [2340] [2341]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5634--5634
[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[]
[2342]
Underfull \hbox (badness 10000) in paragraph at lines 5715--5718
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5726--5726
[]\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[]
[2343]
Underfull \hbox (badness 1622) in paragraph at lines 5763--5768
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
\T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5763--5768
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2344]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5824--5824
[]\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 5825--5825
[] \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 5832--5832
[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[]
[2345]
Underfull \hbox (badness 1062) in paragraph at lines 5961--5964
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2346]
Underfull \hbox (badness 6063) in paragraph at lines 5990--5993
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2347]
Underfull \hbox (badness 2635) in paragraph at lines 6102--6107
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6102--6107
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 6110--6113
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 6220--6230
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6220--6230
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2349]
Underfull \hbox (badness 3179) in paragraph at lines 6302--6305
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2350]
Underfull \hbox (badness 10000) in paragraph at lines 6400--6403
[]\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.,
[2351]
Underfull \hbox (badness 10000) in paragraph at lines 6475--6478
[]\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.,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6491--6491
[]\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
[2352]
Underfull \hbox (badness 2443) in paragraph at lines 6530--6536
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6530--6536
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6551--6554
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2353]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6621--6621
[] \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[]
[2354] [2355]
Underfull \hbox (badness 6268) in paragraph at lines 6757--6760
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
Underfull \hbox (badness 5036) in paragraph at lines 6781--6785
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
. How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6781--6785
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2356] [2357]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again>
\relax
l.6874 \aliasA{det}{Matrix-class}{det}
Underfull \hbox (badness 10000) in paragraph at lines 6977--6980
Underfull \hbox (badness 10000) in paragraph at lines 6987--6989
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2358]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.7050 ...*\%}{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.7158 ...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.7258 ...tcrossprod}{matrix-products}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 7356--7362
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2359] [2360pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7418 \end{Details}
pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox
\fi \fi
l.7418 \end{Details}
]
Underfull \hbox (badness 10000) in paragraph at lines 7429--7432
[]\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 1199) in paragraph at lines 7429--7432
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 7432--7437
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 1371) in paragraph at lines 7432--7437
\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
Underfull \hbox (badness 1502) in paragraph at lines 7437--7441
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
Underfull \hbox (badness 10000) in paragraph at lines 7437--7441
\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
"dgeMatrix")\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 2837) in paragraph at lines 7447--7448
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2361] [2362]
Underfull \hbox (badness 1009) in paragraph at lines 7583--7585
[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
$\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
Underfull \hbox (badness 1062) in paragraph at lines 7628--7631
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
\T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2363]
Underfull \hbox (badness 6063) in paragraph at lines 7662--7665
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2364]
Underfull \hbox (badness 10000) in paragraph at lines 7714--7716
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2365] [2366]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7853--7853
[]\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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Underfull \hbox (badness 2635) in paragraph at lines 7918--7923
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7918--7923
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7926--7929
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2368]
Underfull \hbox (badness 3482) in paragraph at lines 8000--8006
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
that these co-er-cions
[2369]
Underfull \hbox (badness 1867) in paragraph at lines 8120--8122
[]\T1/ptm/m/n/10 fast sim-
[2370]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again>
\relax
l.8160 \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.8160 \HeaderA{norm}{Matrix Norms}{norm}
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8247--8247
[]\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 8248--8248
[]\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 8249--8249
[]\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 8362--8372
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2372]
Underfull \hbox (badness 3179) in paragraph at lines 8433--8436
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2373]
Underfull \hbox (badness 10000) in paragraph at lines 8523--8526
[]\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.,
[2374]
Underfull \hbox (badness 10000) in paragraph at lines 8599--8602
[]\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.,
[2375]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8615--8615
[]\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[]
Overfull \vbox (41.60564pt too high) has occurred while \output is active
[2376]
Underfull \hbox (badness 10000) in paragraph at lines 8725--8727
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
sig-na-tures (use
Underfull \hbox (badness 6493) in paragraph at lines 8727--8730
[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
Underfull \hbox (badness 6428) in paragraph at lines 8733--8740
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2377] [2378]
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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,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8835--8835
[]\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 \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8861--8871
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2379] [2380]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again>
\relax
l.8962 \aliasA{qr}{qr-methods}{qr}
[2381]
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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 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[]
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[]\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[]
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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
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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/p
tm/m/n/10 , it cor-re-sponds to
[2383]
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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"[]
[2384]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war
ning+ ~1.5 sec (2013)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9239--9239
[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.9258 ... the Reciprocal Condition Number}{rcond}
[2385] [2386]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2387] [2388]
Underfull \hbox (badness 10000) in paragraph at lines 9556--9558
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
via one di-men-sional
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\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
not
[2389] [2390]
Underfull \hbox (badness 1558) in paragraph at lines 9707--9710
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2391]
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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:[]
[2392]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again>
\relax
l.9835 \aliasA{solve}{solve-methods}{solve}
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[] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9937--9937
[] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[]
[2393]
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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
Underfull \hbox (badness 10000) in paragraph at lines 9989--9992
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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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 : Checks
if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
[2394]
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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
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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
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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[][][]\T
1/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[]
[2395]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
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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 con-t
rasts to be ap-plied to the
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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
[2396]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
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[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
\T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
be of-
[2397]
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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),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10266--10266
[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2398] [2399]
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[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
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[] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij =
FALSE)[]
[2400]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2401]
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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[]
[2402]
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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)[]
[2403]
Underfull \hbox (badness 10000) in paragraph at lines 10740--10748
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject
of S3 class
[2404]
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[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.10831 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 10961--10963
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/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[]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
[2407]
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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-
Underfull \hbox (badness 3679) in paragraph at lines 11151--11157
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2408]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2409]
Underfull \hbox (badness 10000) in paragraph at lines 11242--11247
[]\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 11257--11259
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2410] [2411]
Underfull \hbox (badness 2698) in paragraph at lines 11382--11388
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2412]
Underfull \hbox (badness 10000) in paragraph at lines 11475--11477
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
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[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11493--11498
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11501--11506
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2413]
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[]\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.,
[2414] [2415]
Underfull \hbox (badness 6641) in paragraph at lines 11659--11662
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
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[]\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
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\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
[2416]
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[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2417] [2418] [2419]
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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
[2420]
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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)[]
[2421] [2422]
Underfull \hbox (badness 6910) in paragraph at lines 12296--12298
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2423] [2424] [2425]) (./boot-pkg.tex [2426]
Chapter 18.
[2427] [2428] [2429] [2430] [2431] [2432] [2433]
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2434]
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[]\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
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[]\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-
[2435] [2436] [2437]
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[]\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.
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[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2438]
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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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[2440]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
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\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply
\T1/pcr/m/n/10 "all"
[2441]
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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
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\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
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2442] [2443] [2444] [2445]
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-
[2446] [2447] [2448] [2449] [2450]
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[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2451] [2452] [2453]
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[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2455]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2456] [2457] [2458]
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[]\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
[2459]
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\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
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[]\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 ,
[2460] [2461]
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/10 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/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
is used. This is mul-ti-plied by
[2462] [2463] [2464] [2465] [2466]
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,[]
[2467] [2468] [2469]
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.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2470]
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))
[2471] [2472] [2473]
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
[2474] [2475] [2476] [2477] [2478] [2479] [2480]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2481] [2482]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2483] [2484] [2485]
Underfull \hbox (badness 10000) in paragraph at lines 4190--4192
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault
is
[2486]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2487] [2488]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4371--4375
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2489] [2490] [2491] [2492] [2493] [2494] [2495] [2496] [2497]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2498] [2499] [2500] [2501]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2502]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2503] [2504] [2505] [2506] [2507] [2508] [2509] [2510]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2511]
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 t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2512]
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 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2513] [2514] [2515] [2516]
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).
[2517] [2518]
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[]
[2519] [2520] [2521]
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
[2522] [2523]
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),[]
[2524] [2525] [2526] [2527] [2528] [2529] [2530] [2531]) (./class-pkg.tex
[2532]
Chapter 19.
[2533] [2534] [2535] [2536] [2537] [2538] [2539] [2540] [2541] [2542] [2543]
[2544] [2545] [2546] [2547] [2548]) (./cluster-pkg.tex
Chapter 20.
[2549]
Underfull \hbox (badness 1655) in paragraph at lines 134--143
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 134--143
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 134--143
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 134--143
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2550] [2551]
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]))[]
[2552] [2553]
Underfull \vbox (badness 10000) has occurred while \output is active [2554]
[2555]
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,
...)[]
[2556] [2557]
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)[]
[2558]
Underfull \hbox (badness 3078) in paragraph at lines 689--692
[]\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
[2559] [2560]
Underfull \hbox (badness 2941) in paragraph at lines 780--783
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 818--818
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
[2561]
Underfull \hbox (badness 10000) in paragraph at lines 865--867
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2562]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 930--930
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2563]
Underfull \hbox (badness 4872) in paragraph at lines 976--978
[]\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 990--994
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2564]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1104--1104
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
[2565]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1121--1121
[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1159--1159
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
[2566]
Underfull \hbox (badness 4144) in paragraph at lines 1191--1195
[]\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
[2567]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1267--1267
[] \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 1273--1273
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2568] [2569]
Underfull \hbox (badness 10000) in paragraph at lines 1412--1417
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 1460--1463
[2570]
Underfull \hbox (badness 10000) in paragraph at lines 1477--1481
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1501--1501
[]\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 1511--1511
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2571]
Underfull \hbox (badness 5741) in paragraph at lines 1551--1554
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2572]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1620--1620
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2573]
Underfull \hbox (badness 1540) in paragraph at lines 1737--1745
\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 =
[2574] [2575]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1828--1828
[]\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 1847--1847
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2576] [2577] [2578] [2579]
Underfull \hbox (badness 10000) in paragraph at lines 2166--2169
[2580]
Underfull \hbox (badness 3179) in paragraph at lines 2180--2186
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2581] [2582]
Underfull \hbox (badness 10000) in paragraph at lines 2338--2341
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2583]
Underfull \hbox (badness 1292) in paragraph at lines 2406--2409
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
Underfull \hbox (badness 6675) in paragraph at lines 2415--2417
[]\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 2438--2441
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2584] [2585] [2586] [2587]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2654--2654
[]\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 ):[]
[2588] [2589] [2590]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2923--2923
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
[2591] [2592]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3026--3026
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2593] [2594] [2595]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3222--3222
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3223--3223
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2596]
Underfull \hbox (badness 10000) in paragraph at lines 3290--3293
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2597]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3340--3340
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3341--3341
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2598] [2599] [2600]
Underfull \hbox (badness 10000) in paragraph at lines 3526--3529
[]\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
[2601]
Underfull \hbox (badness 10000) in paragraph at lines 3589--3594
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2602]
Underfull \hbox (badness 3884) in paragraph at lines 3651--3656
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3663--3666
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2603] [2604] [2605]
Underfull \hbox (badness 10000) in paragraph at lines 3848--3851
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3879--3882
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2606]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3932--3932
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
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[]\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
[2607] [2608] [2609] [2610]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4136--4136
[] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[]
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[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2611] [2612]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4276--4276
[]\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 4285--4285
[] \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 4287--4287
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
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[]\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 4292--4292
[] \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 4299--4299
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2613] [2614] [2615] [2616] [2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 4672--4678
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4688--4690
[]\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
[2619]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4701--4701
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
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[]\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 4713--4713
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4717--4717
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2620]) (./codetools-pkg.tex
Chapter 21.
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[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
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[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
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[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2621]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2622]
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[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2623] [2624] [2625]) (./foreign-pkg.tex [2626]
Chapter 22.
[2627]
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
[2628] [2629]
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 ,
[2630]
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[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2631] [2632] [2633]
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,[]
[2634]
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"),[]
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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
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\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named
to
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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10
,
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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 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2635]
Underfull \hbox (badness 10000) in paragraph at lines 550--558
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 568--574
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2636]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623
[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624
[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2637]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657
[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
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[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2638] [2639]
Underfull \hbox (badness 10000) in paragraph at lines 812--813
Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2640] [2641]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 900--900
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2642]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2643] [2644]
Underfull \hbox (badness 10000) in paragraph at lines 1076--1077
[][][]$\T1/pcr/m/n/10 http : / / 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"))[]
[2645] [2646]
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 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2647]
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 side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2648]) (./lattice-pkg.tex
Chapter 23.
[2649]
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 /
[2650] [2651]
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"),[]
[2652]
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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"),[]
[2653] [2654] [2655] [2656]
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
[2657] [2658] [2659] [2660]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2661]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2662] [2663]
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
[2664] [2665] [2666]
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 ,
[2667]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2668]
Underfull \vbox (badness 10000) has occurred while \output is active [2669]
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
[2670]
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\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10
, etc; see
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
[2671] [2672] [2673] [2674]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
[2675]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2676] [2677] [2678]
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"),[]
[2679] [2680] [2681] [2682] [2683]
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"),[]
[2684] [2685]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2686]
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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 2888--2892
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2894--2896
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
Underfull \hbox (badness 1609) in paragraph at lines 2946--2952
[]\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 2946--2952
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10
changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 2970--2974
[]\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
[2687] [2688]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3073--3073
[] \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 3074--3074
[] \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 3075--3075
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3086--3086
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
[2689]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
Underfull \hbox (badness 2913) in paragraph at lines 3156--3163
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3156--3163
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2690] [2691] [2692] [2693]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again>
\relax
l.3444 \aliasA{parallel}{B\_08\_splom}{parallel}
[2694]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3509--3509
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
[2695] [2696] [2697] [2698] [2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3845--3845
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2700]
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[]\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
[2701] [2702]
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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
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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
[2703]
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\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4183--4187
\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
[2704] [2705]
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4297--4307
\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 4297--4307
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4297--4307
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4297--4307
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
[2706]
Underfull \hbox (badness 1701) in paragraph at lines 4322--4325
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4325--4327
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2707] [2708] [2709] [2710] [2711]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4729--4729
[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2712] [2713]
Underfull \hbox (badness 10000) in paragraph at lines 4916--4919
[]\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 .
[2714] [2715]
Underfull \hbox (badness 1442) in paragraph at lines 5048--5051
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2716] [2717] [2718] [2719] [2720] [2721]
Underfull \hbox (badness 3646) in paragraph at lines 5382--5385
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 ,
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
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[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5413--5413
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2722]
Underfull \hbox (badness 10000) in paragraph at lines 5501--5504
[]\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 5501--5504
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2723]
Underfull \hbox (badness 1635) in paragraph at lines 5527--5532
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2724]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5678--5678
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
[2725]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5692--5692
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5693--5693
[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5696--5696
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5699--5699
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5701--5701
[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5707--5707
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5708--5708
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5709--5709
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5710--5710
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5711--5711
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5727--5729
[]\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 5738--5740
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2726] [2727]
Underfull \hbox (badness 2538) in paragraph at lines 5863--5867
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5874--5881
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5874--5881
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
used (in com-bi-na-tion with
[2728] [2729]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6031
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2730] [2731]
Underfull \hbox (badness 4242) in paragraph at lines 6174--6179
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2732] [2733]
Underfull \hbox (badness 3601) in paragraph at lines 6290--6295
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6290--6295
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2734]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6377--6377
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2735] [2736]
Underfull \hbox (badness 1888) in paragraph at lines 6509--6516
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2737]
Underfull \hbox (badness 10000) in paragraph at lines 6566--6569
[]\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 6566--6569
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2738] [2739] [2740] [2741] [2742] [2743]
Underfull \hbox (badness 1320) in paragraph at lines 6972--6979
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 6972--6979
\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
[2744]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7042--7042
[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
[2745]
Underfull \hbox (badness 10000) in paragraph at lines 7072--7076
[]\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 7072--7076
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 7177--7180
\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
[2747] [2748]
Underfull \hbox (badness 2012) in paragraph at lines 7343--7346
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2749]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7389--7389
[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2750] [2751]
Underfull \hbox (badness 2644) in paragraph at lines 7530--7534
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on
to
Underfull \hbox (badness 2772) in paragraph at lines 7543--7546
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a
list of ar-gu-ments to be sup-plied to
[2752]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7613--7613
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7623--7623
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2753]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7684--7684
[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7689--7689
[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[]
[2754] [2755] [2756]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7874--7874
[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2757]
Underfull \hbox (badness 1436) in paragraph at lines 7929--7935
[]\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
[2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765]
Underfull \hbox (badness 10000) in paragraph at lines 8487--8490
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8487--8490
\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
[2766] [2767]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8662--8662
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8663--8663
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8675--8675
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
[2768]
Underfull \hbox (badness 3118) in paragraph at lines 8694--8697
[]\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
[2769]
Underfull \hbox (badness 1515) in paragraph at lines 8770--8774
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2770]
Underfull \hbox (badness 6316) in paragraph at lines 8876--8881
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2771] [2772]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8983--8983
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2773] [2774]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9122--9122
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2775]
Overfull \hbox (42.94879pt too wide) in paragraph at lines 9181--9185
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
Overfull \hbox (50.63074pt too wide) in paragraph at lines 9181--9185
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2776] [2777] [2778] [2779] [2780] [2781] [2782]
Underfull \hbox (badness 7238) in paragraph at lines 9639--9643
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9639--9643
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
, \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2783] [2784] [2785]pdfTeX warning (ext4): destination with the same identifier
(name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again>
\relax
l.9870 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2786] [2787] [2788]
Underfull \hbox (badness 10000) in paragraph at lines 10032--10037
\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 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10105--10105
[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2789] [2790]) (./mgcv-pkg.tex
Chapter 24.
[2791] [2792]
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,[]
[2793]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 165--165
[] \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
Underfull \hbox (badness 1043) in paragraph at lines 209--214
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2794] [2795] [2796] [2797]
Underfull \hbox (badness 10000) in paragraph at lines 378--385
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 378--385
[][]\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 378--385
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2798]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 421--421
[]\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)+[]
[2799] [2800] [2801]
Underfull \hbox (badness 2922) in paragraph at lines 633--634
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2802] [2803]
Underfull \hbox (badness 2205) in paragraph at lines 703--704
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-i
ng evi-ron-ment vari-able
[2804] [2805]
Underfull \hbox (badness 1158) in paragraph at lines 813--815
[]\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
[2806]
Underfull \hbox (badness 1259) in paragraph at lines 876--877
[]\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).
[2807]
Underfull \vbox (badness 10000) has occurred while \output is active [2808]
[2809] [2810] [2811] [2812]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1224--1224
[]\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 1225--1225
[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1231--1231
[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1238--1238
[]\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
this stratum...[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1240--1240
[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242
[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
[2813]
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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)[]
[2814]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
[2815]
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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$day,to=te)) ## inter
polate to te[]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2824] [2825] [2826] [2827] [2828] [2829] [2830]
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\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
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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 2299--2302
[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
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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
[2831]
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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.
[2832] [2833] [2834]
Underfull \hbox (badness 1043) in paragraph at lines 2503--2509
\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
[2835]
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[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2639--2645
[][]\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 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2836] [2837]
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[2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847]
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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)),[]
[2848] [2849] [2850] [2851] [2852] [2853]
Underfull \hbox (badness 5189) in paragraph at lines 3659--3663
[]\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
[2854]
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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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[2857]
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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
[2858] [2859] [2860] [2861] [2862] [2863] [2864] [2865]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4391--4391
[] \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)+[]
[2866] [2867]
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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,
[2868] [2869]
Underfull \hbox (badness 1142) in paragraph at lines 4667--4671
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2870]
Underfull \hbox (badness 10000) in paragraph at lines 4739--4748
[]\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc
e fail-ures, con-sider mod-i-fy-ing
[2871] [2872]
Underfull \hbox (badness 5970) in paragraph at lines 4856--4862
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1418) in paragraph at lines 4856--4862
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2873]
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[2875] [2876] [2877] [2878]
Underfull \hbox (badness 1577) in paragraph at lines 5208--5211
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2879] [2880] [2881] [2882] [2883] [2884] [2885]
Underfull \hbox (badness 6708) in paragraph at lines 5604--5605
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2886]
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[]
[2887]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5707--5707
[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 5760--5760
[] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[]
[2889] [2890] [2891] [2892] [2893]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
[2894]
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[]\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[]
Underfull \hbox (badness 1142) in paragraph at lines 6120--6124
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2895] [2896] [2897]
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[2899]
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[]\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2)
[2900]
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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)
[2901] [2902] [2903] [2904]
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[2907] [2908]
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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 6893--6893
[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
[2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917]
Underfull \hbox (badness 1242) in paragraph at lines 7436--7437
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2918] [2919]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7523--7523
[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
[2920]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
[2921]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
[2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] [2931] [2932]
[2933] [2934] [2935] [2936] [2937] [2938] [2939]
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Underfull \hbox (badness 10000) in paragraph at lines 8825--8828
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8825--8828
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 8825--8828
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2941]
Underfull \hbox (badness 10000) in paragraph at lines 8881--8884
[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 8881--8884
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
be
[2942] [2943] [2944] [2945]
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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,[]
[2946] [2947]
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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
[2948] [2949]
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[2951]
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[]
[2952]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para-
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\T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c
luded terms,
[2953] [2954]
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
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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[]
[2959]
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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
[2960]
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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
[2961]
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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-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2962] [2963]
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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,
[2964] [2965] [2966] [2967]
Underfull \hbox (badness 1946) in paragraph at lines 10417--10424
[]\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: s
ee
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
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\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2968]
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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)[]
[2969]
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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 ,
[2970] [2971] [2972] [2973] [2974]
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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)
[2975] [2976] [2977] [2978] [2979]
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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,[]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[2981]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
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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
[2984] [2985]
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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 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
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\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
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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 11486--11490
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2986] [2987] [2988]
Underfull \hbox (badness 6876) in paragraph at lines 11681--11687
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
or two vari-ables, spec-i-fied via terms like
[2989]
Underfull \hbox (badness 10000) in paragraph at lines 11722--11723
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2990] [2991]
Underfull \hbox (badness 10000) in paragraph at lines 11839--11840
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2992] [2993]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11893--11893
[] \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 11905--11905
[] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11917--11917
[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11922--11922
[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11928--11928
[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11929--11929
[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[2994]
Underfull \hbox (badness 10000) in paragraph at lines 11998--12000
[]\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 11998--12000
\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
[2995] [2996] [2997]
Underfull \hbox (badness 10000) in paragraph at lines 12126--12127
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[2998]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12207--12207
[]\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 12208--12208
[]\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[]
[2999] [3000] [3001]
Underfull \hbox (badness 10000) in paragraph at lines 12358--12359
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3002] [3003] [3004] [3005]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12597--12597
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3006]
Underfull \hbox (badness 10000) in paragraph at lines 12658--12660
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3007] [3008] [3009]
Underfull \hbox (badness 10000) in paragraph at lines 12817--12820
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 12817--12820
\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 12817--12820
\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"
[3010]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12901--12901
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3011]
Underfull \hbox (badness 10000) in paragraph at lines 12946--12952
[]\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 12946--12952
\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-
[3012] [3013] [3014]
Underfull \vbox (badness 10000) has occurred while \output is active [3015]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13160--13160
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
Underfull \vbox (badness 10000) has occurred while \output is active [3016]
Underfull \hbox (badness 10000) in paragraph at lines 13263--13271
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the
sphere, via terms like
[3017]
Underfull \hbox (badness 10000) in paragraph at lines 13289--13290
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3018] [3019] [3020] [3021]
Underfull \hbox (badness 3396) in paragraph at lines 13550--13553
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
num-ber of vari-ables, spec-i-fied via terms like
[3022]
Underfull \hbox (badness 10000) in paragraph at lines 13595--13597
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3023] [3024] [3025] [3026]
Underfull \hbox (badness 10000) in paragraph at lines 13819--13822
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 13819--13822
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 13852--13856
[][][]\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 13852--13856
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13852--13856
[][]\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 ,
[3027] [3028] [3029] [3030] [3031]
Underfull \hbox (badness 2158) in paragraph at lines 14142--14142
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3032] [3033]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14221--14221
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3034] [3035]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14355--14355
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3036] [3037]
Underfull \hbox (badness 4846) in paragraph at lines 14486--14489
[]\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
[3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048]
[3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15682--15682
[]\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[]
[3058] [3059] [3060]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 15892--15892
[]\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,
[3061]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15894--15894
[]\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 15896--15896
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
Underfull \hbox (badness 10000) in paragraph at lines 15915--15916
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 15915--15916
\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected
by \T1/pcr/m/n/10 ar.row
[3062] [3063] [3064]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16040--16040
[]\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 16041--16041
[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16053--16053
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[3065] [3066] [3067]) (./nlme-pkg.tex [3068]
Chapter 25.
[3069]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3070]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3071] [3072] [3073] [3074] [3075]
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,[]
[3076] [3077]
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 ---------------------------
---------------[]
[3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085]
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"),[]
[3086]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3087] [3088] [3089] [3090] [3091] [3092] [3093]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3094]
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
[3095] [3096] [3097] [3098] [3099]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3100]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
[]\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla
pse = "Dog")[]
[3101]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3102] [3103]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3104]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123]
[3124]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134] [3135]
[3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146]
[3147] [3148]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3149] [3150] [3151] [3152] [3153] [3154] [3155]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\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 ,
[3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\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
[3165]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\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 ,
[3166]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3167]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3168] [3169] [3170] [3171]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\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 ,
[3172]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
[][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3173]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3174]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3175] [3176] [3177]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3178]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3179] [3180] [3181]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3182] [3183] [3184]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7406--7414
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7429--7432
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3185] [3186] [3187]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\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
[3188] [3189] [3190] [3191] [3192] [3193] [3194] [3195]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3196] [3197] [3198] [3199] [3200]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3201]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.8572 \aliasA{sigma}{lmeObject}{sigma}
[3202] [3203] [3204] [3205] [3206]
[3207] [3208] [3209] [3210] [3211] [3212] [3213]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3214]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3215] [3216] [3217] [3218]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again>
\relax
l.9686 ...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.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3219]
Underfull \hbox (badness 10000) in paragraph at lines 9706--9709
[]\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 9750--9753
[]\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 9750--9753
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3220] [3221] [3222] [3223] [3224] [3225] [3226] [3227]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3228] [3229] [3230]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3231]
Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3232] [3233] [3234]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3235] [3236]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3237]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10838--10840
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
[3238] [3239] [3240] [3241]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
[]\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 11131--11131
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
[3242] [3243] [3244] [3245] [3246] [3247]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11521--11521
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3248] [3249] [3250] [3251] [3252] [3253]
Underfull \hbox (badness 6268) in paragraph at lines 11908--11918
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3254] [3255] [3256] [3257]
Underfull \hbox (badness 10000) in paragraph at lines 12169--12175
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3258] [3259] [3260] [3261] [3262]
Underfull \hbox (badness 6876) in paragraph at lines 12491--12493
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
\T1/ptm/m/n/10 will be con-structed from
[3263] [3264]
Underfull \hbox (badness 2452) in paragraph at lines 12647--12654
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3265]
Underfull \hbox (badness 10000) in paragraph at lines 12712--12718
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13301--13301
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3275] [3276] [3277] [3278] [3279]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13666--13666
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3280]
Underfull \hbox (badness 10000) in paragraph at lines 13693--13696
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3281]
Underfull \hbox (badness 1838) in paragraph at lines 13736--13743
[]\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 13736--13743
\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 13793--13793
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3282]
Underfull \hbox (badness 10000) in paragraph at lines 13800--13803
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13800--13803
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13828--13831
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13828--13831
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3283]
Underfull \hbox (badness 10000) in paragraph at lines 13908--13911
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3284]
Underfull \hbox (badness 1472) in paragraph at lines 13933--13940
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3285]
Underfull \hbox (badness 10000) in paragraph at lines 14002--14004
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3286] [3287] [3288] [3289]
Underfull \hbox (badness 1215) in paragraph at lines 14282--14284
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
De-faults to
[3290] [3291] [3292] [3293]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14526--14526
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
[3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302]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.15179 ...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.15179 ...Extract Random Effects}{random.effects}
[3303] [3304] [3305]
[3306] [3307] [3308] [3309] [3310] [3311] [3312] [3313]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15827--15827
[]\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 15846--15846
[] \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 15847--15847
[] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),
tol = 7e-7)[]
[3314]
Underfull \hbox (badness 1009) in paragraph at lines 15877--15886
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3315] [3316]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16024--16024
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
[3317] [3318] [3319] [3320] [3321]
Underfull \hbox (badness 10000) in paragraph at lines 16359--16365
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3322]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16390--16390
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
[3323] [3324] [3325] [3326] [3327] [3328] [3329]
Underfull \hbox (badness 1728) in paragraph at lines 16879--16882
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3330] [3331] [3332] [3333] [3334]
Underfull \hbox (badness 1867) in paragraph at lines 17214--17223
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple 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 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17214--17223
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3335]
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\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance
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\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 1694) in paragraph at lines 17278--17286
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3336] [3337] [3338] [3339]
Underfull \hbox (badness 10000) in paragraph at lines 17525--17532
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3340] [3341] [3342] [3343] [3344] [3345] [3346]
Underfull \hbox (badness 10000) in paragraph at lines 18060--18070
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3347]
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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/ptm/m
/n/10 , in which case a se-quence
[3348]
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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/ptm/m
/n/10 , in which case a se-quence
[3349]
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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/ptm/m
/n/10 , in which case a se-quence
[3350]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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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/ptm/m
/n/10 , in which case a se-quence
[3351]
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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/ptm/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 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18384--18393
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3352]
Underfull \hbox (badness 3579) in paragraph at lines 18423--18428
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3353] [3354]
Underfull \hbox (badness 1009) in paragraph at lines 18569--18578
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3355] [3356]
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\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365]) (./nnet-pkg.tex
[3366]
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
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3367]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3368] [3369] [3370]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3371]
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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)[]
[3372] [3373]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3374]) (./rpart-pkg.tex
Chapter 27.
[3375] [3376] [3377] [3378]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3379] [3380] [3381] [3382]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
at the hor-i-zon-tal plot co-or-di-nates of
[3383] [3384]
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[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
[3385] [3386]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
[3387]
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[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[]
[3388] [3389] [3390]
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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, ...)[]
[3391]
Underfull \hbox (badness 2846) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3392]
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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,[]
[3393] [3394] [3395] [3396] [3397] [3398]
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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 ',
[3399] [3400]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3401] [3402] [3403]) (./spatial-pkg.tex [3404]
Chapter 28.
[3405] [3406] [3407] [3408] [3409] [3410]
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[3411] [3412] [3413] [3414] [3415] [3416] [3417] [3418] [3419] [3420] [3421]
[3422] [3423]) (./survival-pkg.tex [3424]
Chapter 29.
[3425] [3426]
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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.[]
[3427] [3428]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again>
\relax
l.326 ... 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.326 ... Myelogenous Leukemia survival data}{aml}
[3429] [3430]
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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)[]
[3431]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3432] [3433]
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[]\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size,
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3435] [3436]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3437] [3438] [3439]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\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[]
[3440] [3441]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3442]
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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.1177 ...erapy for Stage B/C colon cancer}{colon}
[3443]
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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, ...)[]
[3444] [3445]
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[] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[]
[3446]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3447] [3448] [3449] [3450]
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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:: \T1/pt
m/m/n/10 onto ev-er-thing, in-clud-ing the spe-
Underfull \hbox (badness 10000) in paragraph at lines 1793--1808
\T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t
ime,status) ~ age +
[3451]
Underfull \hbox (badness 1337) in paragraph at lines 1877--1881
[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.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 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3452]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
[3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3461] [3462] [3463]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3464] [3465] [3466] [3467]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3468]
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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"),[]
[3469] [3470]
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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 )))[]
[3471] [3472]
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[] []
[3473] [3474] [3475]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3476] [3477] [3478] [3479] [3480]
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[] \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 )))[]
[3481] [3482] [3483] [3484]
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[3486] [3487]
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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,[]
[3488] [3489] [3490]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3491]
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[]\T1/pcr/m/n/9 mresid <- (lung$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[]
[3492]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3493]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3494] [3495]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3496] [3497]
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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, ...)[]
[3498] [3499] [3500]
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[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3501]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5255--5255
[]\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)) +[]
[3502] [3503] [3504] [3505] [3506]
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[3508] [3509]
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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/ptm/m/n/10
, \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3510] [3511] [3512] [3513] [3514]
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[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[]
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[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.6186 ...ata from a soldering experiment}{solder}
[3515] [3516]
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[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3517] [3518] [3519] [3520] [3521]
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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,[]
[3522] [3523] [3524] [3525]
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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 ),[]
[3526] [3527] [3528]
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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 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3529]
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[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3530] [3531] [3532]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
form
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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample
test, the
[3533]
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[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
[3534]
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[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3535]
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[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3536]
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[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3537] [3538] [3539]
Underfull \hbox (badness 10000) in paragraph at lines 7996--8001
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
[3540]
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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"),[]
[3541] [3542]
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[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3543] [3544]
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[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
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\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
Underfull \hbox (badness 4353) in paragraph at lines 8343--8348
\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
[3545]
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[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3546] [3547] [3548] [3549] [3550]
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[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3551]
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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
[3552] [3553]
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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 surv
reg.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 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 9052--9059
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3554]
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[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3555] [3556] [3557]
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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 )[]
[3558] [3559]
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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 )[]
[3560] [3561] [3562] [3563]
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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[]
[3564]
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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)[]
[3565] [3566] [3567] [3568] [3569] [3570] [3571]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3572] [3573] [3574]) (./fullrefman.ind [3575] [3576] [3577] [3578] [3579]
[3580] [3581] [3582] [3583] [3584] [3585] [3586] [3587] [3588] [3589] [3590]
[3591] [3592] [3593] [3594] [3595] [3596] [3597] [3598]
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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.bs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
[3599]
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[]| \T1/pcr/m/n/10 smooth.construct.ps.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.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 ,
[3600] [3601] [3602] [3603] [3604]
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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.bs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
[3605]
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ps.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.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 ,
[3606]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
[3607] [3608] [3609] [3610] [3611] [3612] [3613] [3614] [3615]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method
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[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method
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[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method
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[]\T1/pcr/m/n/10 [,diagonalMatrix,index,index,logical-method
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[]\T1/pcr/m/n/10 [,diagonalMatrix,index,missing,logical-method
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[]\T1/pcr/m/n/10 [,diagonalMatrix,missing,index,logical-method
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[]\T1/pcr/m/n/10 [,indMatrix,index,missing,logical-method
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[]\T1/pcr/m/n/10 [,sparseVector,index,ANY,ANY-method
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[]\T1/pcr/m/n/10 [,sparseVector,lsparseVector,ANY,ANY-method
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[3616]
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[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,Matrix-method
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[3647]
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[3648]
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-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 rcond,ddenseMatrix,character-method
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[3707] [3708] [3709] [3710] [3711]
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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 tcrossprod,ANY,symmetricMatrix-method
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\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 tensor.prod.model.matrix\T1/ptm/m/it/10 )\T1/p
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[3733] [3734] [3735] [3736] [3737]) (./fullrefman.aux) )
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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 -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-4.0.2/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/exec
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/internet'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/internet'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/lapack'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/lapack'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/X11'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules/X11'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/modules'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/src/library'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/library
installing packages ...
building HTML index ...
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src/library'
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/src'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[1]: Nothing to be done for 'install'.
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/doc/manual'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/doc/manual'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/info
/bin/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-4.0.2/doc/manual'
make: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2'
+ 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-4.0 /usr/lib64/R/doc
+ ln -s ../../share/doc/R-4.0 /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
+ 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/mgcv/libs/mgcv.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/nlme/libs/nlme.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/class/libs/class.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/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/nnet/libs/nnet.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/MASS/libs/MASS.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/foreign/libs/foreign.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/parallel/libs/parallel.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/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/graphics/libs/graphics.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)
/usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -pthread -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -pthread -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:
libR.so -> libR.so
./usr/lib64/R/lib:
Verifying ELF objects in /usr/src/tmp/R-base-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal)
Hardlinking identical .pyc and .pyo files
Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.38601
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-4.0.2
+ export TZ=
+ TZ=
+ make check
make: Entering directory '/usr/src/RPM/BUILD/R-4.0.2'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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' ... OK
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-4.0.2/tests/Examples'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
running strict specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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 '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-4.0.2/tests'
running sloppy specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
running code in 'complex.R' ... OK
comparing 'complex.Rout' to './complex.Rout.save' ... OK
running code in 'eval-etc-2.R' ... OK
comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ... OK
running code in 'print-tests.R' ... OK
comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK
running code in 'lapack.R' ... OK
comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
running code in 'datasets.R' ... OK
comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
running code in 'datetime.R' ... OK
comparing 'datetime.Rout' to './datetime.Rout.save' ... OK
running code in 'iec60559.R' ... OK
comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
checking Sys.timezone ...
make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
running code in 'timezone.R' ...make[4]: *** [Makefile.common:108: timezone.Rout] Error 1
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
Sys.timezone() appears unknown
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
running regression tests ...
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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 '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-4.0.2/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/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-4.0.2/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
running tests of Internet functions
make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
running code in 'internet.R' ... OK
comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247
< Warning message:
< In nsl("cran.r-project.org") :
< nsl() was unable to resolve host 'cran.r-project.org'
---
> >
> > # test do_download (and "record" #{packages}):
> > ap <- available.packages(contrib.url("http://cran.r-project.org"))
> > ## IGNORE_RDIFF_END
> >
> > # test url connections on http
> > zz <- url("http://cran.r-project.org/")
> > readLines(zz)
> [1] "<!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, test http and ftp.
> >
> > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
> V1 V2 V3 V4 V5
> 1 1 307 930 36.58 0
> 2 2 307 940 36.73 0
> 3 3 307 950 36.93 0
> 4 4 307 1000 37.15 0
> 5 5 307 1010 37.23 0
> 6 6 307 1020 37.24 0
> 7 7 307 1030 37.24 0
> 8 8 307 1040 36.90 0
> 9 9 307 1050 36.95 0
> 10 10 307 1100 36.89 0
> 11 11 307 1110 36.95 0
> 12 12 307 1120 37.00 0
> 13 13 307 1130 36.90 0
> 14 14 307 1140 36.99 0
> 15 15 307 1150 36.99 0
> 16 16 307 1200 37.01 0
> 17 17 307 1210 37.04 0
> 18 18 307 1220 37.04 0
> 19 19 307 1230 37.14 0
> 20 20 307 1240 37.07 0
> 21 21 307 1250 36.98 0
> 22 22 307 1300 37.01 0
> 23 23 307 1310 36.97 0
> 24 24 307 1320 36.97 0
> 25 25 307 1330 37.12 0
> 26 26 307 1340 37.13 0
> 27 27 307 1350 37.14 0
> 28 28 307 1400 37.15 0
> 29 29 307 1410 37.17 0
> 30 30 307 1420 37.12 0
> 31 31 307 1430 37.12 0
> 32 32 307 1440 37.17 0
> 33 33 307 1450 37.28 0
> 34 34 307 1500 37.28 0
> 35 35 307 1510 37.44 0
> 36 36 307 1520 37.51 0
> 37 37 307 1530 37.64 0
> 38 38 307 1540 37.51 0
> 39 39 307 1550 37.98 1
> 40 40 307 1600 38.02 1
> 41 41 307 1610 38.00 1
> 42 42 307 1620 38.24 1
> 43 43 307 1630 38.10 1
> 44 44 307 1640 38.24 1
> 45 45 307 1650 38.11 1
> 46 46 307 1700 38.02 1
> 47 47 307 1710 38.11 1
> 48 48 307 1720 38.01 1
> 49 49 307 1730 37.91 1
> 50 50 307 1740 37.96 1
> 51 51 307 1750 38.03 1
> 52 52 307 1800 38.17 1
> 53 53 307 1810 38.19 1
> 54 54 307 1820 38.18 1
> 55 55 307 1830 38.15 1
> 56 56 307 1840 38.04 1
> 57 57 307 1850 37.96 1
> 58 58 307 1900 37.84 1
> 59 59 307 1910 37.83 1
> 60 60 307 1920 37.84 1
> 61 61 307 1930 37.74 1
> 62 62 307 1940 37.76 1
> 63 63 307 1950 37.76 1
> 64 64 307 2000 37.64 1
> 65 65 307 2010 37.63 1
> 66 66 307 2020 38.06 1
> 67 67 307 2030 38.19 1
> 68 68 307 2040 38.35 1
> 69 69 307 2050 38.25 1
> 70 70 307 2100 37.86 1
> 71 71 307 2110 37.95 1
> 72 72 307 2120 37.95 1
> 73 73 307 2130 37.76 1
> 74 74 307 2140 37.60 1
> 75 75 307 2150 37.89 1
> 76 76 307 2200 37.86 1
> 77 77 307 2210 37.71 1
> 78 78 307 2220 37.78 1
> 79 79 307 2230 37.82 1
> 80 80 307 2240 37.76 1
> 81 81 307 2250 37.81 1
> 82 82 307 2300 37.84 1
> 83 83 307 2310 38.01 1
> 84 84 307 2320 38.10 1
> 85 85 307 2330 38.15 1
> 86 86 307 2340 37.92 1
> 87 87 307 2350 37.64 1
> 88 88 308 0 37.70 1
> 89 89 308 10 37.46 1
> 90 90 308 20 37.41 1
> 91 91 308 30 37.46 1
> 92 92 308 40 37.56 1
> 93 93 308 50 37.55 1
> 94 94 308 100 37.75 1
> 95 95 308 110 37.76 1
> 96 96 308 120 37.73 1
> 97 97 308 130 37.77 1
> 98 98 308 140 38.01 1
> 99 99 308 150 38.04 1
> 100 100 308 200 38.07 1
> > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
> V1 V2 V3 V4 V5
> 1 1 307 930 36.58 0
> 2 2 307 940 36.73 0
> 3 3 307 950 36.93 0
> 4 4 307 1000 37.15 0
> 5 5 307 1010 37.23 0
> 6 6 307 1020 37.24 0
> 7 7 307 1030 37.24 0
> 8 8 307 1040 36.90 0
> 9 9 307 1050 36.95 0
> 10 10 307 1100 36.89 0
> 11 11 307 1110 36.95 0
> 12 12 307 1120 37.00 0
> 13 13 307 1130 36.90 0
> 14 14 307 1140 36.99 0
> 15 15 307 1150 36.99 0
> 16 16 307 1200 37.01 0
> 17 17 307 1210 37.04 0
> 18 18 307 1220 37.04 0
> 19 19 307 1230 37.14 0
> 20 20 307 1240 37.07 0
> 21 21 307 1250 36.98 0
> 22 22 307 1300 37.01 0
> 23 23 307 1310 36.97 0
> 24 24 307 1320 36.97 0
> 25 25 307 1330 37.12 0
> 26 26 307 1340 37.13 0
> 27 27 307 1350 37.14 0
> 28 28 307 1400 37.15 0
> 29 29 307 1410 37.17 0
> 30 30 307 1420 37.12 0
> 31 31 307 1430 37.12 0
> 32 32 307 1440 37.17 0
> 33 33 307 1450 37.28 0
> 34 34 307 1500 37.28 0
> 35 35 307 1510 37.44 0
> 36 36 307 1520 37.51 0
> 37 37 307 1530 37.64 0
> 38 38 307 1540 37.51 0
> 39 39 307 1550 37.98 1
> 40 40 307 1600 38.02 1
> 41 41 307 1610 38.00 1
> 42 42 307 1620 38.24 1
> 43 43 307 1630 38.10 1
> 44 44 307 1640 38.24 1
> 45 45 307 1650 38.11 1
> 46 46 307 1700 38.02 1
> 47 47 307 1710 38.11 1
> 48 48 307 1720 38.01 1
> 49 49 307 1730 37.91 1
> 50 50 307 1740 37.96 1
> 51 51 307 1750 38.03 1
> 52 52 307 1800 38.17 1
> 53 53 307 1810 38.19 1
> 54 54 307 1820 38.18 1
> 55 55 307 1830 38.15 1
> 56 56 307 1840 38.04 1
> 57 57 307 1850 37.96 1
> 58 58 307 1900 37.84 1
> 59 59 307 1910 37.83 1
> 60 60 307 1920 37.84 1
> 61 61 307 1930 37.74 1
> 62 62 307 1940 37.76 1
> 63 63 307 1950 37.76 1
> 64 64 307 2000 37.64 1
> 65 65 307 2010 37.63 1
> 66 66 307 2020 38.06 1
> 67 67 307 2030 38.19 1
> 68 68 307 2040 38.35 1
> 69 69 307 2050 38.25 1
> 70 70 307 2100 37.86 1
> 71 71 307 2110 37.95 1
> 72 72 307 2120 37.95 1
> 73 73 307 2130 37.76 1
> 74 74 307 2140 37.60 1
> 75 75 307 2150 37.89 1
> 76 76 307 2200 37.86 1
> 77 77 307 2210 37.71 1
> 78 78 307 2220 37.78 1
> 79 79 307 2230 37.82 1
> 80 80 307 2240 37.76 1
> 81 81 307 2250 37.81 1
> 82 82 307 2300 37.84 1
> 83 83 307 2310 38.01 1
> 84 84 307 2320 38.10 1
> 85 85 307 2330 38.15 1
> 86 86 307 2340 37.92 1
> 87 87 307 2350 37.64 1
> 88 88 308 0 37.70 1
> 89 89 308 10 37.46 1
> 90 90 308 20 37.41 1
> 91 91 308 30 37.46 1
> 92 92 308 40 37.56 1
> 93 93 308 50 37.55 1
> 94 94 308 100 37.75 1
> 95 95 308 110 37.76 1
> 96 96 308 120 37.73 1
> 97 97 308 130 37.77 1
> 98 98 308 140 38.01 1
> 99 99 308 150 38.04 1
> 100 100 308 200 38.07 1
> >
OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2/tests'
make: Leaving directory '/usr/src/RPM/BUILD/R-4.0.2'
+ exit 0
Processing files: R-base-4.0.2-alt1
Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.48959
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-4.0.2
+ DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.2
+ export DOCDIR
+ rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.2
+ /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.2
+ cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.2
+ chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.2
+ chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.2
+ exit 0
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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.J1pibl
find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib)
lib.prov: /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so: 1256 symbols, 21 bpp
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
--- find-provides-deps 2020-08-07 02:04:37.475688776 +0000
+++ filter-provides-deps 2020-08-07 02:04:37.478688686 +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.ojxXMl
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,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
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules/lapack.so: underlinked libraries: /lib64/libdl.so.2
shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh/echo.sh is not executable
find-requires: FINDPACKAGE-COMMANDS: cat grep sh
Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set: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
Requires: /bin/sh, /lib64/ld-linux-x86-64.so.2, coreutils, grep, ld-linux-x86-64.so.2()(64bit) >= set:ihbW3, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426Dgj994wsONU8RZq4ZjETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQZtURAFElDl8totXyLZkjPS80tH2, libXmu.so.6()(64bit) >= set:ljat5WdZ0, libXt.so.6()(64bit) >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1()(64bit) >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJLac4, libc.so.6(GLIBC_2.11)(64bit), libc.so.6(GLIBC_2.14)(64bit), libc.so.6(GLIBC_2.15)(64bit), libc.so.6(GLIBC_2.16)(64bit), libc.so.6(GLIBC_2.17)(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_2.4)(64bit), libc.so.6(GLIBC_2.6)(64bit), libc.so.6(GLIBC_2.7)(64bit), libc.so.6(GLIBC_2.8)(64bit), libcairo.so.2()(64bit) >= set:mgBeCp25NOIyrlQHFsTG1phW01upHNOW8SpbeVohC5Pwchq6KplkgZIPAQh02Zr5HMxPMkimVZpVN9h6QFUdKO6OFjNsjitz641ARaZ5HZAmxdD86kgBnSaNq3ZAVlemZpcoP0tsFeDiZfuQuf3, libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, libdl.so.2(GLIBC_2.2.5)(64bit), libgobject-2.0.so.0()(64bit) >= set:ml6W90, libicui18n.so.67()(64bit) >= set:ro8QoNSM7N8mnCGZIS8D3qcHd0, libicuuc.so.67()(64bit) >= set:pm6zZ0Uf099eu65yc, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQITkXeYooZo0Vt8WFt6QYIOIZmWow6fzRMDwp9MGO0ZhldKUzW8W1RsJZtAeHIPYhIl5WiNVlN8FgR6mScaXXLmW0FDbvWuDSCea0aj0BvFxRc15QVQjV9n85Kyco0a0SzG6SwK1cfwAyHaix50g7p00c0WMF2, 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), libopenblas.so.0()(64bit) >= set:qlsiqIe00icRW574Ku0AAyAyab7fG6SOSAPoPNmLYbhPezMnFyfKftDkkVQaeAYUqnr3WgpZJxDHDDHYiTG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQCfq9fPhNQgw41BExdcI9mdt, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre2-8.so.0()(64bit) >= set:kfq9tJAJZakapZcr8gHlRiHX2PuBva483hqVseVZw6HMZF1, libpng16.so.16()(64bit) >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng16.so.16(PNG16_0)(64bit), libpthread.so.0(GLIBC_2.2.5)(64bit), libreadline.so.7()(64bit) >= set:nidQ8PMktsCwid18OsyEUS8iDQRn5631GOVow7aaRTmMg1UZho7I5k7dG1ZFel4iyBQZd1aPltLOR05Zx8IO0, 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.aM5CZj
Creating R-base-debuginfo package
Processing files: R-full-4.0.2-alt1
Requires: R-devel = 4.0.2-alt1, R-tcltk = 4.0.2-alt1, R-doc-html = 4.0.2-alt1, gcc-c++, gcc-fortran, liblapack-devel, make
Processing files: R-devel-4.0.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.VN1yym
find-provides: broken symbolic link /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool -> ../../../bin/libtool is not going to provide anything
find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,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.maTBhn
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,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) = 4.0.2
Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils
Requires(pre): R-base = 4.0.2-alt1
Requires(postun): R-base = 4.0.2-alt1
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.Nen0nn
Processing files: R-tcltk-4.0.2-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.UXGBFn
find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,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.cl8Ebl
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Provides: tcl(::Utility) = 1.0, tcl(::Utility::dump) = 1.0, tcl(::Utility::expand) = 1.0, tcl(::Utility::number) = 1.0, tcl(::Utility::string) = 1.0, tcl(::Utility::tk) = 1.0, tcl(Hierarchy) = 2.0, tcl(PBar) = 1.0, tcl(Widget) = 2.0
Requires: R-base = 4.0.2-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_2.4)(64bit), libc.so.6(GLIBC_2.7)(64bit), libtcl8.6.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.6.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk)
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.J5kujl
Creating R-tcltk-debuginfo package
Processing files: R-doc-html-4.0.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.sd7QDj
find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.bhfVhm
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Requires: R-base = 4.0.2-alt1
Processing files: R-doc-pdf-4.0.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.P0QiYl
find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.1ErQek
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Conflicts: R-base > 4.0.2, R-base < 4.0.2
Processing files: R-doc-info-4.0.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.Ze1TXl
find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.vYWAwj
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib)
Conflicts: R-base > 4.0.2, R-base < 4.0.2
Processing files: R-base-debuginfo-4.0.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.txuBKm
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.i88zym
find-requires: running scripts (debuginfo)
Provides: debug64(libR.so)
Requires: R-base = 4.0.2-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(libdl.so.2), debug64(libgobject-2.0.so.0), debug64(libicui18n.so.67), debug64(libicuuc.so.67), 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(libpthread.so.0), debug64(libreadline.so.7), debug64(libtiff.so.5), debug64(libz.so.1)
Processing files: R-tcltk-debuginfo-4.0.2-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ZgTZgn
find-provides: running scripts (debuginfo)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.25Knfk
find-requires: running scripts (debuginfo)
Requires: R-tcltk = 4.0.2-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 13 sources provided by R-base-debuginfo
also prunning dir /usr/src/debug/R-4.0.2/include/R_ext
also prunning dir /usr/src/debug/R-4.0.2/src/include
also prunning dir /usr/src/debug/R-4.0.2/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-4.0.2-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-full-4.0.2-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-4.0.2-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-4.0.2-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-html-4.0.2-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-pdf-4.0.2-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-info-4.0.2-alt1.noarch.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-4.0.2-alt1.x86_64.rpm
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-4.0.2-alt1.x86_64.rpm
1875.32user 173.68system 20:25.12elapsed 167%CPU (0avgtext+0avgdata 949088maxresident)k
0inputs+0outputs (0major+20824689minor)pagefaults 0swaps
2066.38user 203.06system 24:05.21elapsed 157%CPU (0avgtext+0avgdata 949088maxresident)k
98576inputs+0outputs (0major+22341070minor)pagefaults 0swaps